HELLO, I WOULD LIKE TO WELCOME
EVERYONE TO ANOTHER INSTALLMENT
OF THE NIH FDA COVID-19
SCIENTIFIC INTEREST GROUP
LECTURE SERIES.
ON BEHALF OF THE STEERING
COMMITTEE IT'S AN HONOR TO
INTRODUCE TODAY'S SPEAKER.
DR. DUNCAN MACCANNELL, IS THE
DIRECTOR OF THE OFFICE OF
ADVANCED MOLECULAR DETECTION,
OAMD, HE HELPS STUDY PATHOGEN
GENOMICS, SCIENTIFIC COMPUTING
AND THE USE OF INNOVATE I REALLY
LABORATORY TECHNOLOGIES ACROSS
THE PUBLIC HEALTH SYSTEM.
DR. MACCANNELL, HOLDS A
BACHELOR'S OF SCIENCE FROM
Mc GILL UNIVERSITY AND EARNED
A MASTER OF BIOTECHNOLOGY AND
Ph.D. IN INFECTIOUS DISEASE
SAYS FROM THE UNIVERSITY OF
CALGARY.
IN 2006 DR. MACCANNELL, BEGAN A
FELLOWSHIP AT CDC PULSE NET AND
SERVED EVER SINCE AS A HEALTH
MICROBIOLOGIST AND A MOLECULAR
EPIDEMIOLOGIST.
HE'S BEEN RECOGNIZED WITH A
ARTHUR S. FLEMMING AWARD, HHS
INNOVATES AWARDS ASSEMBLING'S
PICK AND AN NCZED AWARD.
HE IS A MUCH NEEDED ADVOCATE FOR
THE RAPID, OPEN AND EQUITABLE
CHANGE OF PATHOGEN SEQUENCE DATA
AND HE BROADENS THE SCIENCE,
TRAINING AND EXPERTISE TO HELP
HEALTH PROFESSIONALS IMPROVE
COVID OUTCOMES.
WHEN THE PANDEMIC STRUCK, HIS
ADVOCACY HELPED HIM ESTABLISH
THE EMERGENCY RESPONSE,
EPIDEMIOLOGY AND SURVEILLANCE OR
SPHERES INITIATIVE WHICH SEEKS
TO EXPAND THE USE OF PATHOGEN
GENOMICS TO STRENGTHEN INFECT
YOWZ DISEASE SURVEILLANCE AND
OUTBREAK RESPONSE WHICH IS WHAT
WE WILL BE SPEAKING ABOUT TODAY.
SO WITH THAT WE ARE HONORED TO
HAVE YOU HERE WITH US DUNCAN AND
LEARNING ABOUT YOUR EXPERIENCES
WITH SPHERES.
>> THANK YOU SO MUCH.
I'M GOING TO SHARE MY SCREEN AND
THAT SHOULD WORK.
LOOKS LIKE THAT'S GOOD.
FIRST OF ALL, THANK YOU FOR THE
OPPORTUNITY TO PRESENT TODAY.
I KNOW IT TOOK A LITTLE WHILE TO
GET THE SCHEDULE, IT HAS BEEN A
LONG FEW YEARS, BUT I THINK THIS
IS A REALLY INTERESTING AND
ENLIGHTENING STORY.
IN TALKING ABOUT IT THOUGH, I
WANT TO TRY TO TIE IT INTO WHERE
WE ARE IN THIS MOMENT WITH
PATHOGEN GERONTOLOGYSTS GOMMICS
SURVEILLANCE IN THE U.S. AS WE
THINK ABOUT HOW THESE
TECHNOLOGIES CAN BE APPLIED
GLOBALLY AND HOW WE BUILD THE
NECESSARY INFRASTRUCTURE AND
WORKFORCE AND BROADER
COLLABORATION ECOSYSTEM AROUND
THESE TECHNOLOGIES AND THEIR
APPLICATIONS TO PUBLIC HEALTH, I
TOOK THE ORIGINAL TITLE THEY
SUBMITTED OPTIMISTICALLY IT WAS
A BIT OF A MOUTHFUL AND
CHALLENGING TO PUT ON THE TITLE
SLIDE.
I TIGHTENED IT UP A BIT.
BUT WE WILL TALK MOSTLY ABOUT
NEW PARTNERSHIPS, WE WILL TALK
ABOUT COLLABORATIONS AND HOW HOW
THESE CAME INTO PLAY OVER THE
PAST FEW YEARS.
SO FIRST, I MUST INTRODUCE THE
ADVANCED MOLECULAR DETECTION
PROGRAM, THE COME FROM THE
OFFICE THAT CHAIRS IT, IT WAS
ESTABLISHED IN 2014 AS IN THE
PRESIDENT'S BUDGET AS THE
ADVANCE MOLECULAR DETECTION AND
RESPONSE TO INFECT YOWZ DISEASES
OR AMD BUDGET INITIATIVE.
AT THE TIME IT WAS A
30 MILLION-DOLLAR A YEAR PUBLIC
HEALTH LABORATORY INNOVATION
PROGRAM, IT'S NOW SITTING AT
ABOUT $40 MILLION A YEAR WITH A
FOCUS ON TRANSFORMATIONAL
LABORATORY TECHNOLOGY COMPUTING.
THIRTY, OR $40 MILLION SOUNDS
LIKE A LOT FOR A FEDERAL PROGRAM
BUT WHEN YOU REALIZE THE SCOPE
OF THE MANDATE WHICH IS REALLY
TRANSTHRAITING A LOT OF THESE
EVENTS, TECHNOLOGIES AND
PRACTICE ACROSS ALL THESE CDC
INFECTIOUS DISEASE ACTIVITIES,
ACROSS THE GLOBAL PARTNERS AND
HEALTH SYSTEM, YOU START SLICING
THE PIE RATHER FINELY.
WE LAUNCHED WITH 5 INITIAL KEY
OBJECTIVES, BUT REALLY IF YOU
WANT TO THINK ABOUT AMD, IT'S
EASIEST TO THINK ABOUT IT IN
TERMS OF DOMAINS.
A LOT OF WHAT WE FOCUSED ON IS
ON LABORATORY SEQUENCING OR
GENOMIC SEQUENCING BUT WE'RE NOT
EXCLUSIVELY FOCUS ON THAT, I
THINK A TRUE LINE FOR A LOT OF
WHAT AMD DOES IS AROUND ADVANCED
LABORATORY TECHNOLOGIES, HIGH
COMPLEXITY, GENOMICS,
PROTEOMICS, MULTIOMIC TYPE DATA
SETS AS THEY BECOME PRACTICAL
AND AS THEY BECOME INCORPORATED
INTO PUBLIC HEALTH.
ONE OF THE CONSISTENCIES IN THAT
IS THAT IT OFTEN REQUIRES A LOT
OF EMPHASIS ON CATAANALYSIS, ON
INVESTMENT AND BIO-INFORMATICS,
ON INSURING WE HAVE THE
NECESSARY TECHNICAL
INFRASTRUCTURE IN GOVERNANCE AND
WORKFORCE, NECESSARY TO MAKE ALL
THAT WORK TOGETHER EMPLOY WE
ALSO NEED TO BE ABLE TO
TRANSLATE WHAT THESE TYPES OF
DATA INTO ACTION, WE NEED TO TIE
THIS TO EPIDEMIOLOGY, TIE THIS
TO FRONT LINE PUBLIC HEALTH.
SO THESE REALLY FORM THE 3 MAIN
PILLARS OF THE WORK THAT WE DO.
WE HAVE MULTIPLE AREAS OF
EMPHASIS, SO AS YOU MIGHT
IMAGINE, A THE LO OF WHAT WE DO
IS FOCUSED ON ADVANCED
LABORATORY TECHNOLOGIES, LOOK AT
THEM AS THEY EMERGE, FIGURE OUT
HOW TO STANDARDIZE THEM AS MUCH
AS WE CAN, IMPLEMENTING THEM IN
WELL CENTRAL SOURCED
LABORATORIES LIKE CDC BUT ALSO
IN STATE AND LOCAL PUBLIC HEALTH
DEPARTMENTS ACROSS THE COUNTRY
IN GLOBAL PUBLIC HEALTH LABS
ACROSS THE WORLD.
WE WORK WITH A VARIETY OF
DIFFERENT INSTRUMENT
MANUFACTURES IN DOING SO, WE'RE
ALSO LOOKING AT A LOT OF OTHER
TECHNOLOGIES AS WELL AS THEY
EMERGE, AS THEY BECOME A BIT
MORE PRACTICAL, AS THEY FALL
INTO THIS SORT OF REALM BUT
AGAIN, SORT OF THE UNIFYING
THEME THERE IS THAT MANY OF THEM
ARE VERY DATA INTENSIVE AND MANY
OF THEM REQUIRE SPECIALIZED
SKILLS AND CAREFUL THOUGHT IN
HOW THOSE DATA AND HOW THE
INFORMATION FROM THOSE DATA CAN
BE INCORPORATED INTO PUBLIC
HEALTH.
AND AGAIN, WE'RE NOT JUST
FOCUSING ON WHAT CAN BE SOURCED
IN A SINGLE LAB, WE ARE LOOKING
AT WHAT CAN RUN IN A VARIETY OF
DIFFERENT STATE AND LOCAL HEALTH
DEPARTMENTS OR OUT IN THE FIELD
IF WE HAVE TO ROLL SOMETHING OUT
IN A MOBILE LAB.
WE ALSO DO A FAIR BIT ON THE
REALM OF PUBLIC INFORMATION
TECHNOLOGY, HEALTH I.T. CAN BE
CHALLENGING TO WORK IN, IT'S A
COMPLEX ENVIRONMENT THAT
INVOLVES MULTIPLE DIFFERENT
PARTIES AND CHALLENGES AROUND
THAT AND IT WASPT SET UP
INITIALLY WHEN WE BEGAN THE
PROGRAM TO SUPPORT THINGS LIKE
BIO-INFORMATICS AND HIGH
COMPLIANCE COMPUTING.
WE'VE SINCE HAVE BEEN ABLE TO
STAND UP CAPABILITIES AT CDC, WE
CHAMPIONED A LOT OF EFFORTS AND
PROBABLY TOWARDS THE END OF THE
TALK TODAY I WILL TALK ABOUT THE
UPCOMING CLOUD INITIATIVES THAT
ARE MEANT TO PUSH SOME OF THESE
OUT EENCH FURTHER INTO THE REALM
OF PUBLIC HEALTH.
WE ALSO DO A LOT ON LAB EPIDATA
INTEGRATION, 1 OF THESE THINGS
IS THAT THEY IMENERATE
A--GENOMICS GENERATES A MASSIVE
AMOUNT OF DATA BUT IT IS OFTEN
MACHINE GRADABLE BY DEFAULT.
A LOT OF THE DATA WE NEED TO
INTEGRATE IT WITH THOUGH,
CLINICAL METADATA, EPIDATA,
CLINICIAN NOTES, FIELD NOTES,
THEY'RE OFTEN POORLY STRUCTURED
OR ASYNCHRONOUSLY DRIVED, SO
FIGURING OUT NEW TECHNOLOGIES
AND NEW WAYS TO BRING THESE DATA
TOGETHER EFFECTIVELY AND
EFFICIENTLY HAS BEEN AN ONGOING
CHALLENGE FOR A LOT OF THE WORK
THAT WE DO.
THERE'S BEEN A LOT OF WORK IN
THE PAST FEW YEARS IN DATA
VISUALIZATION AND AND REPORTING,
I WON'T TOUCH ON THOSE HERE BUT
IF YOU THINK ABOUT TI NEVER
WOULD HAVE PREDICTED THAT A FEW
YEARS AGO THAT N TREES AND
DASHBOARDS WOULD BE ON THE FRONT
PAGES AS MAJOR RECORD BUT HERE
WE ARE EMPLOY WE ALSO DO A LOT
OF STRATEGIC COORDINATION AND
PROGRAM SUPPORT.
SO WE PROVIDE FUNDING
ESSENTIALLY INNOVATION AND
ADAPTATION FUNDING TO MANY
DIFFERENT PROGRAMS WITHIN CDC,
IT'S ABOUT 30 OR 40 DIFFERENT
LABORATORY PROGRAMS AND THAT
RANGES FROM LONG-TERM STRATEGIC
TRANSITIONING EXISTING MOLECULAR
SURVEILLANCE METHODS TO GENOMICS
AND OTHER ADVANCED TECHNOLOGIES
TO WHAT WE CALL INCUBATOR
PROJECTS WHICH ARE HIGHER RISK,
HIGH REWARD, R&D TYPE ACTIVITIES
THAT REALLY ENCOURAGE CDC
PROGRAMS TO PUSH THE BOUNDS OF
WHAT THEY'RE ALREADY DOING.
WE DO A LOT OF COORDINATION WITH
STATE BAKE BASED ACTIVITIES AND
INITIATIVES.
A LOT OF PARTNER WORK.
WE WORK EXTENSIVELY ACROSS THE
AGENCY WITH VARIOUS OTHER GROUPS
THAT ARE ACTIVE IN THIS SPACE
AND INCREASINGLY IN GLOBAL
HEALTH.
A LOT OF WHAT WE DO IS ALSO
FOCUSED ON WORKFORCE DEVELOPMENT
SO NOT ONLY MAINTAINING THE
SKILL BASED OF CDC'S WORKFORCE
BUT A LOT OF OUR STATE AND LOCAL
PUBLIC HEALTH PARTNERS, WORKING
ON RECRUITMENT STRATEGY FOR A
LOT OF THESE TECHNICAL SKILLS ON
THE NECESSARY ADMINISTRATIVE
PROCESSES TO MAKE THAT HAPPEN,
THINGS LIKE FELLOWSHIPS AND
OTHER WAYS TO BRING IN THE
TALENT AND NEW SKILLS THAT ARE
DESPERATELY NEEDED TO MAKE THESE
TECHNOLOGIES WORK CENTER FOR
EFFECTIVELY.
LASTLY WE HAD SIGNIFICANT
INNOVATION AND THAT CAN BE
VETTING NEW TECHNOLOGIES WHEN
THEY COME OR IT CAN BE FIGURING
OUT WHERE THE GAPS ARE FOR
IMPLEMENTATION IN THE LAST MILE
FOR TAKING A TECHNOLOGY OUT OF
THE LAB, OUT OF AN IERK DEALIZED
SET OF CIRCUMSTANCES AND BEING
ABLE TO ACTUALLY ARK PLIE IT FOR
PUBLIC HEALTH.
I'M NOT GOING TO TOUCH ON TOO
MUCH OF THAT TODAY BUT IT'S A
GREAT TOPIC THAT I WOULD LOVE TO
TALK ABOUT LATER.
SO LET'S TALK ABOUT WHERE WE
STARTED AND WHERE WE ARE TODAY,
AND THEN I'LL EASE US INTO THE
COVID-19 RESPONSE.
IF YOU LOOK BACK IN 2013, THERE
REALLY WERE ONLY 6 OR 7 STATE OR
LOCAL PUBLIC HEALTH DEPARTMENTS
THAT HAD NEXT GENERATION
SEQUENCING CAPABILITY AND IN
MANY OF THOSE STATES, THE
SEQUENCERS WEREN'T ACTUALLY
LOCATED AT THE STATE PUBLIC
HEALTH DEPARTMENT.
AT THE TIME, MANY HEALTH STATE
PUBLIC HEALTH DEPARTMENTS DIDN'T
HAVE THE NECESSARY
INFRASTRUCTURE WHETHER
FACILITIES OR THE PERSONNEL THAT
WERE TRAINED AND ABLE TO
DEDICATE THE NECESSARY TIME
RESOURCES TO THESE NEW
INSTRUMENTS.
A LOT OF THESE INITIAL
PLACEMENTS WERE AROUND FOOD BORN
DEC SURVEILLANCE SO THINGS LIKE
PULSE NET AND FDA'S GENOME
TRACKER, BUT YOU KNOW--TOOK OFF
AND ENABLED BY SOME OF THESE
PROGRAMS AND DEFINITELY DRIVEN
BY AMD INVESTMENT.
BY 2018, EVERY STATE AND PUBLIC
HEALTH DEPARTMENT IN THE COUNTRY
HAD SEQUENCING CAPABILITY, MANY
COUNTY AND LOCAL PUBLIC HEALTH
DEPARTMENTS ALSO HAD THAT KIND
OF CAPABILITY.
AND AGAIN, A LOT OF THE INITIAL
INVESTMENT WAS FOCUSED ON FOOD
BORNE DISEASE SURVEILLANCE BUT
ONCE THERE, OTHER CDC PROGRAMS
AND OTHER LOCAL AND STATE DRIVEN
SURVEILLANCE AND ACTIVITY
STARTED TO TAKE ADEVAPORATAGE OF
THESE CAPABILITIES AND THE
KNOWLEDGE THAT CAME WITH THEM
EMPLOY MANY STATES FOCUSED ON
INFLUENZA, HEALTHCARE ASSOCIATED
INFECTIONS, THINGS LIKE VIRAL
HEPATITIS, TUBERC CUEULOSEIS TO
NAME A FEW BUT YOU STARTED TO
SEE REALLY AN ADOPTION AND
EXPLORATION OF THESE
TECHNOLOGIES ALONG WITH EFFORTS
TO TRY AND STANDARDIZE AND BUILD
CONSISTENT SURVEILLANCE
STRUCTURE ON TOP OF THEM.
SO, YOU KNOW IF YOU ARE LOOKING
AT THIS MAP, YOU MIGHT THINK
THAT THE COUNTRY, OR THE U.S.
PUBLIC HEALTH SYSTEM WAS WELL
POSITIONED TO USE PATHOGEN
GENOMICS AS AN APPROACH FOR AN
ONCOMING PANDEMIC EVENT BUT YOU
KNOW WHAT WE FOUND, BY THE END
OF 2021, SO ESSENTIALLY OR I
GUESS THAT'S 20--SORRY THAT
WOULD BE TART OF 2024, A FULL
YEAR INTO THE PANDEMIC, ONLY
LESS THAN HALF OF THE STATE
PUBLIC HEALTH DEPARTMENTS HAD
SUBMITTED EVEN A SARS-COV-2
SEQUENCE TO ANY OF THE PUB
LIAISON REPOSITORIES OR TO CDC.
THERE HAD BEEN FEDERAL
SEQUENCING BUT YOU KNOW MANY OF
THE STATE PUBLIC HEALTH
DEPARTMENTS ISSUES EVEN THOUGH
THE SEQUENCING CAPABILITY WAS IN
PLACE, IT WAS OFTEN BUILT AROUND
SPECIFIC PROGRAMS AND THE
CAPACITY WAS DEEP BUT NARROW.
AND SO WHEN FACED WITH A NEW AND
EMERGING CHALLENGE AND A NEW
PATHOGEN, IT WASN'T ALWAYS
STRAIGHT FORWARD TO PIVOT THESE
RESOURCES TO ADAPT TO ONCOMING
THREAT.
SO WHAT DID WE SEE, BY THE END
OF 2020, THERE WERE JUST UNDER
20 MILLION REPORTED U.S. CASES,
THERE WERE ABOUT FEIVE THOUSAND,
JUST OVER 57,000 SEQUENCES IN
USAID AT THE TIME, A FEWER THAN
THAT IN GENBANK AND THAT
ENCLUEDED ABOUT 20 STATE AND
PUBLIC HEALTH LABS SO DEFINITELY
LESS THAN HALF.
AND AN INTERESTING THING YOU'LL
NOTE HERE IS THAT OVER HALF THE
SEQUENCES GENERATED DURING THAT
FIRST YEAR WERE NOT FROM STATE
OR FEDERAL PUBLIC HEALTH
ACTIVITIES, THEY WERE FROM
EITHER PRIVATE SECTOR LABS OR
ACADEMIC AND CLINICAL
LABORATORIES THAT HAD ACCESS TO
PATIENT SAMPLES THAT BEGAN
SEQUENCING BUT THERE WEREN'T
NECESSARILY CONNECTED TO THE
PUBLIC HEALTH RESPONSE AT ANY
LEVEL.
AT THE CDC, WE STARTED WITH 2
DIFFERENT APPROACHES, FIRST WAS
TO REALLY START PUTTING TOGETHR
USEFUL INFORMATION FOR OUR STATE
AND ACADEMIC PARTNERS THAT WERE
BEGINNING TO SEQUENCE THE VIRUS.
AT THE--ESPECIALLY IN THE EARLY
DAYS OF THE RESPONSE, THERE WERE
MANY DIFFERENT PROTOCOLS THAT
WERE STARTING TO EMERGE, THERE
WERE BIOINFORMATIC TOOLS THAT
WERE STARTING TO BE DEVELOPED
AND REFINED AND SO 1 THE INITIAL
THINGS WE FELT WAS GOING TO BE
USEFUL WAS TO SET UP AN
INFORMATION CLEARINGHOUSE FOR
SOME OF THESE PIECES OF DATA.
TO DO SO, GIVEN SOME OF THE
CHALLENGES TIMES OF GOVERNMENT
CLEARANCE PROCESSES AND THE FACT
THAT THIS IS REALLY MEANT TO BE
A CROWD SOURCED PIECE OF
INFORMATION OR A SOURCE OF
INFORMATION, WE WENT TO CDC'S
GITHUB REPOSITORY AND SET UP A
GITHUB PAGE THAT WAS WRITTEN AND
MARKED DOWN.
IT ALLOWED FOR ONGOING
CONTRIBUTION, ONGOING EFCLIEWGZ
OF THIS PAGE AS MORE AND MORE
INFORMATION CAME ON.
ADDITIONAL CONTRIBUTORS COULD
PROPOSE YOU KNOW ADDITIONAL
CHANGES OR PUSH CHANGES TO THE
PAGE OR SUBMIT THEM AND AT THE
END OF THE DAY, WE ENDED UP
MAKING ABOUT 330 COMMITS TO THIS
IN THE FIRST YEAR OR SO OF THE
PANDEMIC JUST OVER 20 DIFFERENT
CONTRIBUTORS SUBMITTED CONTENT
TO IT THAT WE REVIEWED AND
INCLUDED.
THIS INCLUDED UPDATES TO R-DEC
PROTOCOLS, CHANGES IN NEW
BIOINFORMATIC TOOLS, BOTH OPEN
SOURCE AND PROPRIETARY THAT WERE
AVAILABLE, INCLUDED IMPORTANT
REFERENCES, IT ALSO INCLUDED
SOME INITIAL RECOMMENDATIONS FOR
HOW TO HANDLE SOME OF THE
METADATA ISSUES AROUND SEQUENCE
DATA SHARING BECAUSE 1 OF THE
CHALLENGES THAT WE'VE SEEN, YOU
KNOW ESPECIALLY WITH THE
INCREASED OPENNESS OF SEQUENCE
DATA SHARING, HAS BEEN VARIOUS
LEVELS OF COMFORT AND VARIOUS
LEVELS OF CHALLENGE AROUND
SHARING PARTICULARLY THE
METADATA ASSOCIATE WIDE THOSE
SEQUENCES.
THE MOST SALIENT EXAMPLE I
USUALLY GO BACK TO IS BEFORE THE
PANDEMIC, SALMONELLA WAS
ROUTINELY SEQUENCED AS PART OF
THE FOOD BORNE DISEASE
SURVEILLANCE AS WELL AS LISTERIA
AND SALMONELLA AND OTHER FOOD
BORNE PATHOGENS BUT MANY OF
THESE DIDN'T INCLUDEITATE LEVEL
GEOLOCATION BECAUSE THERE WERE
CONCERNS THAT YOU KNOW BY MANY
OF THE SUBMITTERS THAT THERE WAS
NOT NECESSARILY THE LEVEL OF
COMFORT WITH SHARING THAT LEVEL
OF METADATA.
IN MANY CASES YOU WEREN'T
LOOKING AT THINGS LIKE POTENTIAL
REIDENTIFIABILITY OF INDIVIDUAL
PATIENTS BUT CERTAINLY, HAVING
STATE LEVEL DATA WAS SOMETHING
THAT PEOPLE NEEDED TO ACTUALLY
WRAP THEIR HEADS AROUND.
THAT CHANGED DRAMATICALLY WITH
THE PANDEMIC.
WE SAW MANY JURISDICTIONS
SHARINGITATE LEVEL, BUT TIMES
COUNTY LEVEL INFORMATION.
IF THE DATA AND THEIR OVER SIGHT
AND GORCHANCE PERMITTED THAT BUT
1 THING WE DID DO IS STANDARDIZE
HOW VIRUSES WERE NAMED THEY WERE
SUBMITTED BASED ON SOME OF THE
EARLY CDC'S MENTIONS.
PART OF THE RATIONAL FOR DOING
THIS WAS TO GET CONSISTENCY SO
RECOMMENDATIONS FOR HOW SOME OF
THE METADATA CAN BE COMPLETED
BUT ALSO HOW WE CAN ACTUALLY
MAKE SOME OF THE VIRAL DATA A
BIT MORE USEFUL AND UNIQUE
APPROACH FOR A CONSISTENT WAY
FOR THESE NOMENCLATURES THAT WAS
CONSISTENT WITH ICTV RECOMMEND
ANTICIPATIONS AND OTHER CURRENT
GUIDANCE BUT SAT THE SAME TIME
GAVE ENOUGH INFORMATION THAT IF
ALL OTHER METADATA FOR SEQUENCE
WAS LOST, AN INDIVIDUAL COULD
STILL TRACK DOWN WHICH STATE IT
CAME FROM AND THE LAB THAT
SUBMITTED IT AND A SAMPLE, A
USEFUL SASMEM OF NUMBERS,
EMBEDDING SOME OF THE MOST
CRITICAL METADATA INTO THE NAME
OF THE VIRUS ITSELF.
THIS IS A CONVENTION THAT TOOK
HOLD AND WAS ACTUALLY ENDED UP
BEING PRETTY USEFUL BUT IT WAS
AN EXAMPLE OF APPLYING SOME
FAIRLY EARLY, FAIRLY GENTLE
RECOMMENDATIONS AND AND SEEING
WHERE THAT COULD POTENTIALLY GO.
THE OTHER THING WE DID WAS TO
START SEEING WHETHER WE COULD
ACTUALLY ORGANIZE THE EFFORTS
THAT WERE CURRENTLY ONGOING.
THERE WERE PROBABLY ABOUT A
DOZEN, MAYBE 2 DOZEN
LABORATORIES ACROSS THE UNITED
STATES THAT HAD BEEN SEQUENCING
REGULARLY AND SO 1 OF THE FIRST
EFFORTS WAS REALLY TO SEE
WHETHER WE COULD ACTUALLY
CONNECT ALL OF THESE DIFFERENT
GROUPS INTO A COMMUNITY
PRACTICE.
SO THIS INCLUDED A RANGE OF
DIFFERENT FOLKS, IT'S FROM CDC
LABS TO STATE AND LOCAL PUBLIC
HEALTH, ACADEMIC AND CLINICAL
NUMBER OF PRIVATE SECTOR
ENTITIES WERE ON THIS AS WELL AS
REPRESENTATIVES FROM MAJOR
REPOSITORIES LIKE NCBI, AND
[INDISCERNIBLE].
THE INITIAL OUTREACH WAS REALLY
MEANT TO SEE WHETHER WE BEING
ACTUALLY NOT NECESSARILY CROWD
SOURCE BUT HELP SHAPE A LOT OF
THESTS THAT WERE CURRENTLY
ONGOING TO TALK ABOUT DATA AND
METADATA STANDARDS TO MAKE SURE
WE WERE HAVING CONSISTENT
CONVERSATIONS AROUND THAT WE
COULD MAKE THE BEST USE OUT OF
DATA THAT WAS BEING GENERATED
THE OTHER PIECE IS THERE WERE
JUST NOT ANY CONNECTED AT THE
LOWER LEVEL AND SO THERE WAS A
LOT OF DATA GENERATION GOING ON
BUT WITHOUT THAT SORT OF
CONNECTION OR FOLLOW THROUGH, IT
WAS POSSIBLE THAT YOU KNOW THAT
THESE SEQUENCING EFFORTS WOULD
BECOME STAMP COLLECTING EFFORTS
QUICKLY AND NOT NECESSARILY TIED
TO ACTIONABLE PUBLIC HEALTH
OUTCOMES.
SO THIS INITIATIVE TOOK OFF, IT
WAS ABOUT A DOZEN DIFFERENT
GROUPS, AND IT TARTED REALLY TO
SNOWBALL MORE QUICKLY THAN I
THINK WE ANTICIPATED INITIALLY
THE THOUGHT WAS TO BRING
TOGETHER THIS GROUP TO START
TALKING ABOUT AND APPROACHES TO
REALLY CONNECT THESE MORE
CONSISTENTLY TO PUBLIC HEALTH AS
TIME WENT ON THOUGH THE
CONTRIBUTING CONTINUED TO GROW.
THE SPHERES ITSELF WAS AND IS A
TECHNICAL COMMUNITY OF PRACTICE,
IT'S MEANT TO PROVIDE A VENUE
FOR NETWORKING AND COLLABORATION
ISSUES IT'S MEANT TO TIE
TOGETHER A LOT OF THESE
DESPERATE SEQUENCING EFFORTS AND
LABS THAT ARE INVOLVED IN THIS
TO PROVIDE RAPID COMMUNICATION
BETWEEN THESE DIFFERENT LABS AND
TO ALLOW FOR MUCH MORE FLUID
PUBLIC HEALTH ENGAGEMENT AND
SHARING OF EXPERTISE.
IT ALLOWED US TO BETTER ALIGN
ACEM DICK AND PRIVATE SECTOR
SEQUENCING EFFORTS WHICH WERE
REALLY NEW TO THE PUBLIC HEALTH
DOMAIN, OFTEN PUBLIC HEALTH
LABORATORY TESTING HAPPENS IN A
BIT OF A SILO, WE WORK WITH MANY
CLINICAL LABS, MANY ACADEMIC
PROVIDERS THAT'S USUALLY AROUND
SPECIFIC PATHOGEN, SPECIFIC
APPLICATIONS, THIS WAS A UNIQUE
SET OF CIRCUMSTANCES WHERE, YOU
KNOW ACADEMIC AND PRIVATE SECTOR
LABS WERE STARTING TO ACTIVELY
GENERATE FAIRLY LARGE AMOUNTS OF
USEFUL DATA WITHOUT NECESSARILY
HAVING THAT FACTOR.
WE HAVE DIFFERENT PRACTICES BUT
WE GAVE REGULAR VARIANT UPDATES
OR WE GIVE REGULAR VARIANT
UPDATES ON THE CURRENT STATE OF
ESSENTIALLY THE OPEN DATA THAT'S
OUT THERE. SOME OF THE
INTERPRETATIONS AND VIEWS OF CDC
DASHBOARDS AND SOME OF THE OTHER
PIECES OF INFORMATION THAT
CAPTURE VARIANT DATA A LOT OF
REPORTS ON CURRENT OUTBREAK
INVESTIGATIONS AND SURVEILLANCE
RESPONSE AND ONGOING TOPICAL
EVENTS, WHETHER IT'S A NUMBER OF
TALKS ON RETURN TO SCHOOL AND
SOME OF THE VARIANT SURVEILLANCE
ON COLLEGE CAMPUSES AND ACADEMIC
INSTITUTIONS IN VARIOUS
CONGREGATE SETTINGS, VARIOUS
APPROACHES AND BIOINFORMATIC
TOOLS THAT HAS BEEN DEVELOPED
OVER THE YEARS AS WELL.
AND VARIOUS DISCUSSIONS ON
APPROACHES AND ANALYSIS AND DATA
SHARING A LOT OF DISCUSSION ON
LABORATORY AND BIOINFORMATIC
METHODS AND WE TRY TO CREATE AN
ENVIRONMENT THAT INCORPORATED
NOT ONLY PUBLIC HEALTH AND
ACADEMIC DEVELOP AMS AND R&D BUT
ALSO IN AN EQUITABLE MANNER,
REPRESENTATIVES FROM THE PRIVATE
SECTOR AS NEW KITS WERE
DEVELOPED, AS NEW TOOLS WERE
THERE, WE TRIED TO MAKE SURE
THAT THINGS THAT WERE USEFUL HAD
AN OPPORTUNITY TO BE SHOWCASED
TO A TECHNICAL AUDIENCE.
WE ALSO HAD THE OPPORTUNITY TO
TALK PRETTY EXTENSIVELY ABOUT
DATA AND METADATA STANDARDS SO
WE WORKED WITH GROUPS LIKE SAGE
AND THE PUBLIC HEALTH ALLIANCE
FOR EPIDEMIOLOGY TO DEVELOP DATA
STANDARDS.
WORKED WITH DID NCBI TO ACTUALLY
IMPLEMENT THEM AND THESE HAVE
BEEN PUT ON THE BACK END FOR
BOTH ISOLATES AND NCBI AS WELL
AS WASTE WATER BASED
EPIDEMIOLOGY WHICH I THINK IS AN
IMPORTANT STEP FOR INSURING
THERE'S THE NECESSARY STRUCTURE
THERE.
IT ALSO ALLOWED US TO TAYLOR A
LOT OF CDC'S RESOURCES WE COULD
REACH OUT TO OUR RESOURCES OVER
THE PANDEMIC.
IT ALLOWED US TO HAVE VERY
DIRECT ENGAGEMENT WITH NOT ONLY
THE SEQUENCERS THEMSELVES BUT A
LOT OF THE TOOL DEVELOPERS, SO
THE DEVELOPERS OF NEXT STRAIN
AND MICROREACT AND OTHERS AND
OUTBREAK.INFO AND MANY OTHER
PLATFORMS WERE ACTIVELY INVOLVED
IN THESE CONVERSATIONS AND
ACCESSIBLE THROUGH THE SPHERES
AND OTHER CHANNELS WHICH MEANT
THAT OUR--AS THE COMMUNITY GREW,
COMPLEXITY OF THESE TASKS
CONTINUED TO MOVE.
THERE WAS AN OPPORTUNITY FOR
ONGOING DIALOGUE FOR FUTURE
REQUESTS AND FOR ONGOING
ANALYSIS.
AS TIME WENT ON, I WILL TALK
ABOUT RESOURCES IN A SECOND, BUT
IT ALLOWED US TO HAVE A LITTLE
BIT MORE TARGET WHEN WE'RE
THINKING ABOUT SURVEILLANCE,
RESEARCH FUNDING AND SUPPORT, SO
WE STARTED USING BROAD AGENCY
ANNOUNCEMENTS AND I WILL TALK
ABOUT THAT IN A MOMENT, BUT IT
ALLOWED US TO NOT ONLY ADVERTISE
THOSE BUT TO CREATE THOSE SORTS
OF OPPORTUNITIES THAT I THINK
REALLY HELPED BUILD AND FOSTER
THIS EARLY ACADEMIC PRIVATE
SECTOR, PUBLIC SECTOR
COLLABORATION.
IT ALSO ALLOWED FOR US TO WORK
ON IMPROVING INFRASTRUCTURE AND
RESOURCES SO AS THE CDC
DASHBOARD CAME OUT, IT GAVE
OPPORTUNITIES FOR FEEDBACK AND
PRIORITIZATION, USER
ACCEPTABILITY TESTING ON SOME OF
THE DATA RESOURCES WE WERE
MAKING AVAILABLE.
FEEDBACK ON SOME OF THE CONTEXT
AND COMMUNICATIONS EFFORTS THAT
WERE HAPPENING AROUND SOME OF
THESE VARIANTS.
AND MORE OVER PROVIDED A FORUM
WHERE WE COULD TALK PRETTY
CANDIDLY ABOUT WHEN THE GENOMIC
EPI WAS SAYING, WHAT IT WASN'T
SAYING, THE KNOWNS AND UNKNOWNS
AT THE TIME.
IT WAS HELPFUL TO HELP GUIDE THE
ACADEMIC CONVERSATION AND
BROADER PUBLIC CONVERSATION
AROUND VARIANTS AS THEY EMERGED.
THE FORMAT ITSELF WAS RELATIVELY
STRAIGHT FORWARD, WE STARTED OFF
WITH WEEKLY ZOOM CALLS, IT HAS
GRADUALLY DWINDLED TO BI-WEEKLY
AND MONTHLY CALLS ABOUT YOU
THEY'RE STILL VERY ACTIVELY
ATTENDED SO ABOUT 205 HELPED
PARTICIPANTS USUALLY.
WE HAVE VARIOUS TOPICS AND GUEST
SPEAKERS.
WE MAINTAIN AN ACTIVE GITHUB AND
MULTIPLE DIFFERENT GITHUB
PROJECTS WITHIN THAT AND AN
ACTIVE WORK SPACE WHICH ACTS AS
MISSION CONTROL FOR A LOT OF
THESE DISCUSSIONS.
SO WE STARTED OUT WITH A FEW
DOZEN FOLKS HONESTLY, IF YOU
WERE ASKING ME 4 YEARS AGO, HOW
BIG THIS EFFORT WOULD GET, I
WOULD HAVE TOLD YOU MAYBE A
HUNDRED, MAYBE 200 PEOPLE WOULD
BE INVOLVED AT THE END OF THE
DAY.
YOU KNOW AS THE PANDEMIC ROLLED
ON.
TODAY, IT'S OVER 1800 SCIENTISTS
REPRESENTING MORE THAN 200
ORGANIZATIONS, THIS IS AN OLDER
SLIDE BUT IT DOES GIVE YOU A
SENSE OF THE BREDTH OF
PARTICIPATION, THE TYPES OF
PARTICIPATION THAT ARE NOT ONLY
ACROSS U.S. GOVERNMENT AND
PUBLIC HEALTH, BUT ACROSS THE
PRIVATE SECTOR IN ACADEMIA AS
WELL.
SO OUR FOCUS HAS STARTED TO
EXPAND A LITTLE BIT.
A LOT OF THIS WAS INITIALLY
FOCUSED ON SARS-COV-2, SEQUENCE
ANALYSIS AND SURVEILLANCE BUT WE
HAVE STARTED TO BROADEN OUR
FOCUS ON OTHER PATHOGENSAs
WELL.
WHEN THE INITIAL CASES OF THE
MPOX WERE REPORTED THERE WAS A
LOT OF ONGOING DISCUSSION AND
UPDATES FROM NOT ONLY THE MPOX
VIRUS GROUP AT CDC BUT ALSO FROM
A NUMBER OF DIFFERENT GROUPS
ACROSS THE U.S. THAT WERE EITHER
CONDUCTING FRONT LINE PUBLIC
HEALTH SURVEILLANCE AND GENOMIC
SURVEILLANCE BUT ALSO RESPONSE
WORK.
I WILL IMAGINE THAT WE WILL
CONTINUE TO EXPAND THIS SORT OF
MISSION BECAUSE A LOT OF THE
THEMES THAT WE COVER, A LOT OF
THE EFFORTS THAT HAVE REALLY
BEEN BUILT, A LOT OF THIS
ECOSYSTEM AND COLLABORATION
ENVIRONMENT IS REALLY FOCUSED ON
GENOMIC EPIDEMIOLOGY AND
BUILDING THIS KIND OF CAPABILITY
ACROSS MULTIPLE SECTORS.
SO THINGS CHANGED SOMEWHAT
MARKETEDLY WHEN THE BIDEN
ADMINISTRATION ANNOUNCED A
$1.21 MILLION INVETMENT IN
SURVEILLANCE AS PART OF THE
AMERICAN RESCUE PLAN.
BEFORE THAT WE HAD BEEN DOING
WITH A LARGELY SHOE STRING
BUDGET AND MOSTLY RELYING ON
SEQUENCING THAT WAS HAPPENING AT
CDC, A HANDFUL OFITATE AND LOCAL
HEALTH DEPARTMENTS THAT WERE
ABLE TO ALLOCATE THE RESOURCES
AND THIS NETWORK OF ACADEMIC
PARTNERS THAT WERE DOING AND
ACTUALLY QUITE FORMIDABLE JOB.
AS YOU CAN SEE, SEQUENCE OUTPUT
ROSE DRAMATICALLY WITH THE
INJECTION OF THESE ADDITIONAL
RESOURCES.
AS OF THIS WEEK, U.S. LABS HAVE
SUBMITTED ABOUT 5.1 MILLION
SEQUENCES TO GISAID, THEY
SUBMITTED ABOUT 3.6 MILLION
SEQUENCES TO GENBANK AND THAT IS
IMPORTANT BECAUSE MANY OF THESE
LABS, MANY U.S. LABS INCLUDING
ALL THE FEDERAL EFFORTS ARE
SUBMITTING TO MULTIPLE
REPOSITORIES TO INSURE MAXIMUM
OPENNESS AND AVAILABILITY OF THE
DATA.
AND THIS NUMBER'S A BIT OUT OF
DATE, I APOLOGIZE, I GOT AN
UPDATED NUMBER FROM THE NCBI
JUST YESTERDAY, BUT I FAILED TO
UPDATE IT HERE, I THINK WE'RE
ALMOST AT 3 MILLION SEQUENCES IN
SRA, WHICH IS FANTASTIC TO SEE.
JUST TO GIVE YOU A SENSE OF
OVERALL PROPORTIONS, ACTUALLY I
DO THAT ON THE NEXT SLIDE, IT'S
ABOUT 16 MILLION SEQUENCES RIGHT
NOW IN GISAID, WHICH MAKES
SARS-COV-2 1 OF THE MOST
EXTENSIVELY SEQUENCED PATHOGENS
IN HISTORY IF NOT THE MOST.
ABOUT 16 MILLION SEQUENCES,
ABOUT 31% OR JUST OVER 5 MILLION
ARE FROM U.S. CASES, ABOUT 21%,
ABOUT OVER A FIFTH OF ALL THE
SEQUENCES THERE ARE FROM LOCAL
STATE AND PUBLIC HEALTH
SURVEILLANCE SO BEEN ABLE TO
SUPER CHARGE THAT PRETTY
EXTENSIVELY AND A FULL
1.3 MILLION, A BIT MORE THAN
THAT NOW, OR ABOUT 8%, 8-9% ARE
FROM THE ACADEMIC AND CLINICAL
LAB
LABORATORIES AND YOU CAN SEE THE
BREAK DOWN IN DARK BLUE HERE,
ORANGE AND FEDERAL SEQUENCING
ACTIVITIES, LIGHT BLUE ARE
ACADEMIC AND CLINICAL, AND YOU
CAN SEE THAT ACADEMIC AND
CLINICAL HAS PLAYED AN IMPORTANT
ROLE.
YOU ALSO SEE A SHOT OF PINK
THROUGH A LOT OF THIS AND THAT
IS PRIVATE SECTOR SEQUENCING
THAT HAS OCCURRED VIRTUALLY
THROUGHOUT THE PANDEMIC, AT
VARIOUS LEVELS FOR VARIOUS
PURPOSES.
NOT ALL OF THESE DATA ARE
NECESSARILY USEFUL FOR PUBLIC
HEALTH SURVEILLANCE.
WE DO HAVE STANDARDIZED METADATA
TEXT IN THE DATA TO TRY AND
CAPTURE SOME OF THE MORE
REPRESENTATIVE POPULATION
SEQUENCES IF WE CAN BECAUSE SOME
MAY BE CAPTURED FOR A SPECIFIC
STUDY OR FROM SPECIFIC COHORT OF
PATIENTS OR FROM AN OUTBREAK
INVESTIGATION WHICH MAKES THEM A
LITTLE BIT LESS USEFUL, A LOT
LESS USEFUL FOR NATIONAL
SURVEILLANCE, BUT, YOU KNOW,
THESE--THIS IS AN ENORMOUS BODY
OF WORK AND CERTAINLY, YOU KNOW
I WANT TO TALK IN A MOMENT ABOUT
THE VALUE OF THIS RESEARCH
ECOSYSTEM AND THE POTENTIAL OF
BLENDING NOT ONLY PUBLIC HEALTH
SURVEILLANCE BUT OPEN DATA
COLLECTION.
SO THE OTHER THING I WANT TO
EMPHASIZE IS THAT THERE ARE
DIFFERENT OBJECTIVES AND
PRIORITIES FOR SEQUENCE DATA
OPERATING IN DIFFERENT LEVELS.
YOU KNOW SPHERES REALLY WAS
MEANT TO TRY AND STITCH
TOGETHER, DRAW TOGETHER, ALL OF
THESE PUBLIC HEALTH AND
NONCONVENTIONAL PUBLIC HEALTH
PARTNERS THAT WE'RE SUDDENLY
FOUND THEMSELVES SEQUENCING.
IT ALLOWED FOR A FLUID PLATFORM
WHERE WE COULD SHARE
INFORMATION, WHERE WE COULD
FACILITY WHERE NEEDED AND
RAPIDLY REALLOCATE RESOURCES IF
THAT MADE SENSE, IT ALLOWED US
TO SHARE CAPACITY, PRIORITIZE
SOME OF OUR OWN EFFORTS, AND
IMPROVE THE UTILITY, QUALITY AND
TIMELINESS OF THE QUALITY
INFORMATION BEING GENERATED
EMPLOY WE PUT IN PLACE A NUMBER
OF DIFFERENT FEDERAL ACTIVITIES
SO CDC'S NSTHEIR, OR SARS-COV-2
SURVEILLANCE PROGRAM IS KEENED
OF A CONVENTIONAL NATIONAL
SURVEILLANCE EFFORT,ITATE PUBLIC
HEALTH DEPARTMENTS SEND IN A
REGULAR REPRESENTATIVE SET OF
POSITIVE SPECIMENS THEY RECEIVE
ETCH MONTH.
THEY COME IN TO CDC AND RUN
THROUGH A STAN ARDIZEED SET OF
PIPELINES AND ARE SEEN IN A
FAIRLY CONSIST EPT WAY.
IT BIFFS US A FAIRLY BASE LINE
HEART BEAT OF CIRCULATING
BIODIVERSITY IN THE COUNTRY AND
REALLY NOT THAT DIFFERENT FOR
WHAT HAPPENS FOR FLU
SURVEILLANCE AND OTHER VIRAL
PATHOGENS.
ONE ADDITION THAT REALLY ALLOWED
US TO ACCELERATE THING SYSTEM
THE INCLUSION OF THE COMMERCIAL
LABS, REALIZING THAT IN MANY
WAYS, SEQUENCING VIRUSES IS
SOMETHING THAT IS SOMETHING THAT
CAN BE COMODITIZED, IT'S NOT A
HIGHLY SPECIALIZED FUNCTION.
IN MANY CASES IT'S ACCESS TO
APPROPRIATE AND REPRESENT NEW
SPECIMENS THAT IS THE BIGGEST
CHALLENGE FOR EFFECTIVE
SURVEILLANCE.
BY WORKING WITH SOME OF THE
NATIONAL LABS, SOME OF THE
BIGGER NATIONAL LABS, AT 1 POINT
WE WERE WORKING WITH 9 DIFFERENT
LARGE SCALE REGIONAL OR NATIONAL
LABORATORIES, NOW WE'RE DOWN TO
3.
IT ALLOWED FOR CAPTURE OF
POSITIVE SPECIMENS FROM A VERY
WIDE FOOTPRINT CROSS THE
GEOGRAPHY FROM THE UNITED STATES
FROM A VARIETY OF DIFFERENT
CONTEXT, FROM PHARMACIES TO
PHYSICIAN'S OFFICES TO TERTIARY
CARE, AND ALLOWED US TO GET A
REALLY MORE COMPREHENSIVE
COMPLETE VIEW OF WHAT WAS GOING
ON AND WHAT WAS CIRCULATING.
AT A NATIONAL LEVEL, THE GOAL IS
REALLY TO PROVIDE NATIONAL BASE
LINE MONITORING AND VARIANCE
SURVEILLANCE TO HELP WITH RISK
ASSESSMENT, ALLOCATE RESOURCES
TO ASSESS THE EFFICACY OF
VACCINES AND THERAPEUTIC ANDS
HELP MAKE THOSE LARGER
DECISIONS.
BUT WE ALSO REALIZED THAT IN
THINKING ABOUT SPHERES AND
THINKING ABOUT ALL THE DIFFERENT
DATA,--DATA CAPTURE SEQUENCING
EFFORTS THAT WERE HAPPENING
AROUND THE COUNTRY, WE ALSO
NEEDED TO ACCOMMODATE THE USES
AT STATE AND LOCAL PUBLIC HEALTH
LEVEL, SO MAKING SURE THAT LOCAL
SURVEILLANCE MONITORING FOR
OUTBREAK INVESTIGATIONS, CONTACT
TRACING WHERE APPROPRIATE,
INFECTION CONTROL PRACTICES
COULD ALSO MAKE USE OF THESE
DATA.
ONE OF THE CHALLENGES THAT THIS
HAD WAS, YOU KNOW A LOT OF THE
NATIONAL DATA IS DEIESH
DENTIFIED AT THAT LEVEL, WE HAD
TO BUILD IN MECHANISMS TO,A LOW
FORITATE AND LOCAL PUBLIC HEALTH
DEPARTMENTS TO PERFORM
REIDENTIFICATION OF CASES OR BE
ABLE TO LINK THEM WITH MORE
DETAILED METADATA SO THEY COULD
USE SOME OF THESE FEDERALLY
GATHERED SEQUENCES IN PART OF
THEIRITATE AND LOCAL RESPONSE
ACTIVITY.
I TALKED ABOUT MULTIPLE
SUBMISSIONS AND THE IMPORTANCE
OF THAT, YOU KNOW 1 THING THAT I
THINK I WOULD LIKE TO UNDERSCORE
IS WE'VE BEEN WORKING ON A LOT
OF THE TOOLING TO TRY TO MAKE
THIS EASIER TO TRY AND MAKE
CONSISTENT METADATA A MUCH MORE
ACTIVE REALITY AND TO INSURE
THAT THE DATA WE'RE GENERATING,
YOU KNOW IN SUPPORT OF NOT ONLY
PANDEMIC RESPONSE BUT IN
TAXPAYER FUBDED EFFORTS, SHOULD
BE MAXIMALLY USEFUL AND NOT ONLY
FOR PUBLIC HEALTH, BUT IDEALLY
RESEARCH AND R&D.
LET'S LOOK AT THE DIRECTION
THINGS ARE GOING AND TO DO SO, I
WANT TO SHOW THIS RELATIVELY
SIMPLE CARTOON OF HOW PATHOGEN
GENOMICS AND GENOMICS
SURVEILLANCE WORK IN A LOT OF
DIFFERENT CONTEXT, SO FROM
PATIENTS YOU HAVE PRIMARY
DIAGNOSTIC TESTING THAT CAN
HAPPEN IN A VARIETY OF DIFFERENT
SETTINGS, SOME OF THOSE SAMPLES
ARE MOVING FORWARD TO MORE
ADVANCED OR ESOTERIC TESTING
WHICH INCLUDES SEQUENCING.
IDEALLY YOU HAVE A GOOD
INTEGRATION WITH SEQUENCING, THE
BIO-INFORMATICS CORE TO ACTUALLY
MAKE AND EXPERTISE NEEDED TO
TURN THOSE DATA INTO MEANINGFUL
INFORMATION.
YOU HAVE THE GOOD ENGAGEMENT
WITH THE EPIDEMIOLOGIST AND IN
DOING SO, YOU CAN BRING IN
MULTIPLE DIFFERENT TYPES OF DATA
AND TAKE THAT REALTIME OR NEAR
REALTIME PATHOGEN GENOMIC DATA,
CONTEXTURAL DATA, OTHER DATA
SOURCES AND USE THAT TO DERIVE
EFFECTIVE PUBLIC HEALTH ACTION.
FOR MOST OF WHAT WE DO IN PUBLIC
HEALTH, THIS NEEDS TO BE THE
NORTH STAR, WHAT IS THE PUBLIC
HEALTH OUTCOME THAT IS DESIRED,
HOW DO WE WORK BACKWARDS TO
FIGURE OUT WHAT DATA, HOW MUCH
DATA, THE TYPE AND GRANULARITY
OF THE TYPE THAT WE NEED TO GET
TO THAT POINT.
THE PAST FEW YEARS HAVE SEEN AN
EXPLOSION OF DIFFERENT SOURCES
FROM WHICH SEQUENCE DATA CAN BE
DERIVED.
WE'VE SEEN WASTE WATER
SURVEILLANCE REALLY TAKE OFF,
WASTE PAWRT MONITORING IS NOT
NEW, IT'S BEEN USE INDEED POLIO
SURVEILLANCES, MANY PEOPLE KNOW
FOR DECADES, THE EXPANSION INTO
THE NATIONAL WASTE WATER
SURVEILLANCE SYSTEM AND
EXPANSION GLOBALLY, INTO
INCORPORATING WASTE WATER, BASED
EPIDEMIOLOGY AS A MONITOR AND
STRATEGY REALLY PRESENTS AN
EXCITING NEW OPPORTUNITY FOR
POPULATION BASED SURVEILLANCE,
YOU KNOW ALTHOUGH I THINK--WHEN
THE DATA CAN BE INFORMATIVE WHEN
IT NEEDS TO BE INCORPORATED WITH
OTHER SOURCES OF DATA AND YOU
KNOW WHEN IT CAN POTENTIALLY NOT
BE AS HELPFUL AS IT COULD BE.
WE'VE SEEN ALSO THE
EXPANSION--I'M NOT GOING TO TALK
ABOUT THE TRAVELER GENOMIC
PROGRAM TODAY BUT LOOKING AT
SWABBING SOME OF THE NOT ONLY
WASTE WATER ON AIRCRAFTS BUT
SWABBING SOME OF THE TRAVELING
PUBLIC AND USING THAT AS THE WAY
TO FOR TRACE TRANSMISSION OF
SARS-COV-2 AND OTHER VIRUSES.
WE HAVE SEEN THIS IN MANY AREAS
OF HEALTH AND MANY REPOSITORIES
HAVE IT FROM HERE AND SPILL
OVERS, SPILL BACK, ALL THESE
NEED TO BE INCORPORATED INTO
VARIOUS STRATEGIES.
IDEALLY THOUGH YOU WANT TO MAKE
SURE YOU'RE DRIVING AS MUCH--AND
I REALIZE THAT NOT EVERY PUBLIC
HEALTH ENTITY, NOT EVERY
SUBMITTER WILL BE IN A POSITION
TO SUPPORT THIS BUT BEING ABLE
TO SUPPORT OPEN DATA AND OPEN
SCIENCE, THIS IS SOMETHING THAT
WE FEEL VERY STRONGLY ABOUT IN A
LOT OF THE U.S. PUBLIC HEALTH
DATA GENERATION, CREATING THIS
SORT OF DATA SHARING ECOSYSTEM,
REALLY DRIVES RESEARCH AND
INNOVATION AND I HAVE NO DOUBT,
THAT HOPEFULLY COUNTLESS
Ph.D.s AND GRADUATE WORK
WILL BE DONE ON THE BACKS OF A
LOT OF THE SEQUENCE DATA BEING
GENERATED BY U.S. PUBLIC HEALTH
LABS OVER THE COURSE OF THE PAST
FEW YEARS.
THAT OBVIOUSLY NEEDS TO BE TIED
INTO AN IMPORTANT CONVERSATION
AROUND ETHICS AND PATHOGEN
ACCESS AND BENEFIT SHARING BUT
YOU KNOW I THINK THERE'S
TREMENDOUS VALUE IN OPEN DATA
AND I THINK THERE'S WAYS TO DO
IT RESPONSIBLY WHILE STILL
ALLOWING INITIAL SUBMITTERS TO
HAVE FULL ACADEMIC LICENSE TO
TAKE ADVANTAGE OF A LOT OF THE
CONTEXT AND STORY THAT
THEY--THAT ONLY THEY CAN TELL
AND TO BE ABLE IT ACTUALLY PUT
THOSE DATA OUT THERE.
SO IF YOU DO THIS RIGHT, IT
HELPS INFORM BETTER STRATEGIES,
IT HELPS YOU DEFINE WHERE YOU
NEED TECHNOLOGICAL IMPROVEMENT,
IT HELPS YOU IDENTIFY NEW
APPROACHES FOR DIAGNOSTICS, NEW
TARGETS OR EVALUATE THE 1S THAT
ARE OUT THERE AND HELPS YOU
REFINE AND MODEL YOUR
SURVEILLANCE, UNDERSTANDING HOW
TO SCALE SURVEILLANCE, AND WHERE
YOU NEEDED THE DEFINITE
APPROACHES AND THE DIFFERENT
MOLECULAR TECHNIQUES.
ONE OF THE EMERGES REALITIES IS,
YOU KNOW WE ALSO HAVE TO THINK
ABOUT HOW CLINICAL AND REFERENCE
REPORTING FITS INTO THIS, WITH
SOME OF THE UPCOMING POTENTIAL
CHANGES AROUND LDTs, WITH
ONGOING CONVERSATIONS AROUND THE
USE OF PATHOGENIC, METHON DONNIC
METHODS AND CLIA AND OTHER
CREDITED FACILITIES WE NEED TO
MAKE SURE AS WE BUILD THESE
SYSTEMS, BUILD THESE DATABASES,
AS WE THINK ABOUT HOW THIS
CONTINUUM WORKS, THERE NEEDS TO
BE THE NECESSARY AUDITTABILITY
AND CONTROLS BUILT IN TO BE
COMPLIANT WITH REGULATORY
REPORTING REQUIREMENTS.
ALL OF THIS, YOU KNOW REQUIRES
ONGOING INVESTMENT IN PEOPLE, IN
INFRASTRUCTURE AND TECHNOLOGY,
AND SYSTEMS, GOVERNANCE FOR
SURE, QUALITY IS USUALLY
SOMETIMES, MAYBE--MAYBE
SOMETIMES AN AFTER THOUGHT BUT
NEEDS TO ENGRAINED IN ALL LEVELS
OF THIS, BUT YOU KNOW I THINK
WE'VE SEEN THE VALUE OF BRINGING
IN MIEW PARTNERS, FRESH THINKING
ON THIS, AND REALLY TAKING
ADVANTAGE OF THE SYNERGYS THAT
THAT BRINGS.
SO I'M GOING TO FAST FORWARD
THROUGH THIS IN THE INTEREST OF
TIME, 1 THING I WANT TO
HIGHLIGHT THOUGH IS THERE ARE
LOTS OF DIFFERENT CHALLENGES AT
EVERY SINGLE PHASE OF GENOMIC
SURVEILLANCE BUT THERE ARE 2
IMPORTANT TRUTHS.
ONE THESE ARE VERY UNIVERSAL,
THEY ARE APPLIED TO VETERINARY
COMMUNITIUALLY ANY PATHOGEN
WE'RE INTERESTED IN AND
SURVEILLING FOR.
THE ACTUAL NUANCE AND SPECIFICS
OF THE CHALLENGES MAY DIFFER A
LITTLE BIT, BUT A LOT OF THEM
ARE VERY SOLVABLE IF WE WORK
ACROSS IN SORT OF A CROSS
CUTTING WAY.
THE OTHER PIECE IS THAT THIS
JUST DOESN'T APPLY TO U.S. LABS
OR WELL RESOURCED U.S. LABS,
THESE ARE UNIVERSAL TRUTHS,
UNIVERSAL CHALLENGES, ALSO
UNIVERSAL OPPORTUNITIES, AS WE
LOOK AT THE CHALLENGES AROUND
THE WORKFORCE, AROUND CAPACITY
DEVELOPMENT, AROUND INSURING
NECESSARY QUALITY SYSTEMS AND IT
IN PLACE, AS WE BUILD THE
NECESSARY TOOLS FOR REPORTING
AND DATA INTEGRATION, THESE ARE
CHALLENGES THAT ARE SHARED BY A
LOT OF OUR GLOBAL PARTNERS AND
IN MANY CASES MANY OF OUR GLOBAL
PARTNERS HAVE COME UP WITH
REALLY EVENNIVE WAYS OF
ADDRESSING THESE CHALLENGES SO I
THINK WE'RE IN A UNIQUE POINT IN
LABORATORY METHOD ANDS PUBLIC
HEALTH DEVELOPMENT WHERE I THINK
THERE'S AN OPPORTUNITY FOR REAL
GLOBAL CONVERSATION AROUND SOME
OF THESE CHALLENGES, HOW WE CAN
IMPROVE THEM, IMPROVE
INTEROPERABILITY AND HOW
TOGETHER WE CAN SOLVE SOME OF
THE CHALLENGES.
SO IN THE TIME THAT REMAINS I
WANT TO TALK A LITTLE BIT ABOUT
THE FUTURE--POTENTIAL XUR KIND
OF WHAT THIS BRINGS.
A LOT OF WHAT I TALKED ABOUT IS
THE NEW PARTNERSHIPS ISSUES THE
ROLE OF NEW PARTNERSHIPS, THE
IMPACT THAT HAS HAD AND LESSONS
LEARNED FROM THAT, I WANT TO
TAKE US BACK NOW TO TALK ABOUT
HOW WE APPROACHED THE REGIONAL
MODELS IN THE PROBLEM OF
IMPLEMENTING TECHNOLOGIES AND
PUBLIC HEALTH AND A LITTLE BIT
ABOUT WHERE WE'RE GOING IN THE
FUTURE.
SO FIELD FUNCTIONS GO BACK UP,
ABOUT 5 OR 6 YEARS, WE HAD TAKEN
AMD TAKEN A REGIONAL MODEL TO
BUILDING THIS KIND OF
CAPACITY,RY WEALZ WE COULD BT
PUT A BIOINFORMATITION AND
GENOMIC EPIDEMIOLOGIST IN EVERY
SINGLE STATE ASK LOCAL PUBLIC
HEALTH DEPARTMENT IN THE COUNTRY
BUT WE COULD AT LEAST TAKE A
REGIONAL APPROACH TO THIS AND
START FUNDING THESE POSITIONS TO
HELP IDENTIFY REGIONAL
PRIORITIES TO ACT AS A REGIONAL
TECHNIICAL RESOURCE AND HELP
DESK IN SOME CASES AND TO HELP
IDENTIFY, PLAN AND EVALUATE
THINGS LIKE TRAINING AND
CAPACITY BELLING.
THIS HELPED US NOT ONLY HAVE
PEOPLE IN THE FIELD THAT COULD
ACTUALLY PRACTICALLY AND
HANDS-ON WORK ON THESE
CHALLENGES BUT ALSO TO HELP US
PRIORITIZE WHERE WE NEEDED TO
MAKE OR TO FOCUS OUR EFFORTS AND
RESOURCES.
THE PAST FEW YEARS GIVEN AN
INJECTION OF FUNDING TO BUILD
GENOMIC SURVEILLANCE IT ALLOWED
US TO MAKE INVESTMENTS IN STATE
AND LOCAL HEALTH DEPARTMENTS, SO
MANY HAVE HAD THE OPPORTUNITY TO
BUILD STRONGER AND MORE ADAPT
BELIEVE INFRASTRUCTURE, HIRE
MORE LABORATORY STAFF,
SPECIALIZED LABORATORY STAFF TO
START BUILDING BIO-INFORMATICS
TEAMS AND STRENGTHENING GENOMIC
EPIDEMIOLOGY GROUPS ACROSS
THEIR--CROSS THEIR HEALTH
DEPARTMENTS.
THIS IS TRUE YOU KNOW FOR
LARGE
STATES AND IT'S ALSO TRUE FOR
SMALL COUNTY AND LOCAL HEALTH
DEPARTMENTS THAT HAVE TAKEN
ADVANTAGE OF THIS INFLUX OF
RESOURCES TO HELP AND GUIDE AND
START BUILD THIS CAPABILITY.
SO SOME OF THIS WAS THINGS LIKE
CAPITAL INVESTMENTS, INSURING WE
HAVE THE NECESSARY BUILDINGS AND
YOU KNOW FACILITIES TO ACTUALLY
SUPPORT THESE KINDS OF
INSTRUMENTATION, THESE KINDS OF
DATA DEMANDS.
SOME OF IT IS INVESTMENTS IN
LABORATORY TECHNOLOGY ITSELF,
INCLUDING AUTOMATION, MAKING
SURE THAT SAMPLE PROCESSING CAN
PROCEED TO PAY.
BUT A LOT OF IT IS IN BUILDING
THE NECESSARY WORKFORCE TO
ACTUALLY DO THE WORK AND TO MAKE
SURE THAT WE ACTUALLY HAVE
HIGHLY SKILLED PEOPLE IN ALL THE
PLACES THAT WE ACTUALLY NEED
THEM ACROSS THE PUBLIC HEALTH
SYSTEM IN ORDER TO MAKE THIS
WORK.
IT'S ALSO ALLOWED US TO PUSH
DOWN THE LESSONS FROM THE
SPHERES TO THE STATE AND LOCAL
LEVEL.
WE'RE DOING A LOT OF THINGS, WE
WILL TALK ABOUT A FEW HOPEFULLY
IN A MINUTE, ABOUT BUILDING THIS
REACTION SERVICE BETWEEN
ACADEMIA AND THE PRIVATE SECTOR,
AND THAT CONTINUES TO BE AN
IMPORTANT THEME.
HOW CAN WE CONTINUE TO
STRENGTHEN THIS, HOW CAN WE
INSURE THAT GRADUATES FROM THE
ACADEMIC PROGRAMS CONSIDER
PUBLIC HEALTH IS NOT AN
ALTERNATIVE CAREER BUT PERHAPS A
VITAL AND INTERESTING CAREER
PATH THAT THEY MIGHT CONSIDER
FROM DAY 1 OF THEIR PROGRAMS.
IT ALSO ALLOWS US TO INSURE THAT
A LOT OF THESEITATE AND LOCAL
PUBLIC HEALTH DEPARTMENTS HAVE
ACCESS TO THESE PLATFORMS,
WHETHER IT'S FEDERALLY FUNDED,
COORDINATED SURVEILLANCE TOOLS
OR WHETHER THAT IS NEW DATA
DASHBOARDS, NEW DATA INTEGRATION
BOARDS THAT ALLOW THEM TO DO
THEIR WORK MORE EFFECTIVE
LOAMACYY AND SHARE THE DATA MORE
EFFECTIVELY AMONG THEIR TEAMS,
ALL OF THESE HAVE REALLY BECOME
POSSIBLE AND YOU KNOW OUR FED BY
NOT ONLY THESE INVESTMENTS BUT A
LOT OF THE PARTNERSHIPS THAT
COME WITH IT.
WE ALSO USE BROAD AGENCY
ANNOUNCE WANTS PRETTY
EFFECTIVELY, BEFORE 2020 WE USED
EXACTLY 1 BROAD AGENCY
ANNOUNCEMENT.
WE USED IT TO DEVELOP A SET OF
TOOLS WITH THE CDPS, OR THE
OXFORD BIG DATA INSTITUTE, SET
OF TOOLS CALLED DATA FLOW WHICH
REALLY ACT AS AN ETL LAYER FOR
METADATA AND DATA
TRANSFORMATION.
OVER THE COURSE OF THE PANDEMIC,
WE PUT OUT 44 ADDITIONAL VA
PROJECTS OR 45 BAA PROJECTS, IN
THE EARLY DAYS THIS WAS IN SOME
WAYS BOLSTERED OUR SARS-COV-2
SURVEILLANCE ACTIVITIES, IT HAD
A MECHANISM THAT COULD SUPPORT
CLINICAL EFFORTS THAT WERE
PROVIDING USEFUL DATA AND INPUT.
AS TIME WENT ON, IT STARTED TO
FOCUS MORE ON SARS-COV-2 VARIANT
CHARACTERIZATION AND ANALYSIS,
UNDERSTANDING VACCINE EFFICACY
AND OTHER IMPORTANT
CHEARKTISTICS AS THEY CAME
ALONG.
IT'S SINCE BROADENED WE'VE HAD
INCREASED FOCUS AND RECENT
SOLICITATIONS ON BIO-INFORMATICS
SOFTWARE, TOOLS FOR N AND FILE O
DYNAMIC ANALYSIS AND WASTE WATER
AND ANALYSIS TOOLS AND IN OUR
MOST RECENT SOLICITATION, WHICH
IS ACTUALLY CLOSING THIS FROM A
LOT OF IT IS FOCUSED ON
PATHOGENIC AGNOSTIC AND/OR
METAAND REALLY TRYING TO PUSH
THE INFOIVATION ENVELOPE A
LITTLE BIT BUT TO DO SO IN A WAY
THAT IS CONDUCTED BACK TO STATE
AND FEDERAL PUBLIC HEALTH.
A LOT OF THING VS COME OUT OF
THE VAs, SOME OF THIS SOME OF
THIS IS RESEARCH AROUND
SARS-COV-2 EXPW I SHOULD COME UP
WITH A PUBLICATION LIST OF
EVERYTHING THAT'S SUPPORTED AS A
RESULT OF THIS, IT ALLOWED FOR
THE DEVELOPMENT AND
IMPLEMENTATION OF A LOT OF NEW
TOOLS AND CAPABILITIES AS I
SAID, YOU KNOW, THE
IMPLEMENTATION OF SOME OF THESE
TOOLS AT THE STATE AND LOCAL
PUBLIC HEALTH DEPARTMENT HAS
CHANGED THEIR ABILITY TO USE IT
EFFECTIVELY AND TO INCORPORATE
THAT NOT ONLY IN THE SARS-COV-2
RESPONSE AS WELL.
A LOT OF THESE ARE PARTIAL
SUPPORT AND DEVELOPMENT OF THE
LOT OF THE NEW TOOLS FOR
DENATIONAL LIBRARY OF MEDICINIC
EPIDEMIOLOGY--TOOLS LIKE THE
UPDATER LYING INFRASTRUCTURE
HAVE BEEN DEVELOPED AND ARE
INDISPENSABLE AS WELL AS NEW
VISUALIZATION TOOLS THAT ALLOW
FOR RAPID INTERPRETATION OF
DATA.
SOME OF THIS HAS HELPED FILL
GAPS, A SINGLE BAA PROJECT WAS
RESPONSIBLE FOR OVER HALF OF THE
SEQUENCES THAT WERE GENERATED
FROM A SINGLE UNDERREPRESENTED
STATE, YOU KNOW THE STATE PUBLIC
HEALTH DEPARTMENT JUST WAS
HAVING CHALLENGES GETTING HANDS
ON THE NECESSARY SAMPLES
EMPLOY--MULTISTATE REGIONAL
CLINICAL VIERPTS THIS IS A POST
MASTERS POST DOCTORAL FELLOWSHIP
PROGRAM, IT'S BEEN AN
OPPORTUNITY FOR US TO USE A TOOL
OR PLATFORMS LIKE SPHERES TO
ADVERTISE FOR THESE KINDS OF
OPPORTUNITIES, WE RECENTLY
ENTERED INTO PARTNERSHIP 2 WITH
THE FERGUSON FELLOWSHIP PROGRAM
WHICH SPECIFICALLY, NOT
SPECIFICALLY BUT IT HELPS TO
BUILD YOU KNOW UNDERREPRESENTED
GROUPS WITHIN PUBLIC HEALTH TO
MATCH THOSE AND WE'RE STARTING
TO BUILD OUT A RECRUITMENT
INFRASTRUCTURE TO MAKE SURE WE
ACTUALLY--I SAID INFRASTRUCTURE
A LOT, A RECRUITMENT FOUNDATION
THAT ALLOWS US TO BRING IN A LOT
OF DIFFERENT PEOPLE FROM
DEFINITE BACKGROUNDS AND
DIFFERENT SKILL SETS AND CAN
HELP BUILD OUT BIO-INFORMATICS
BUT GENOMIC AND EPIY AND
LABORATORY TECHNIQUE.
THE MAJORITY OF THEM NOW
AREITATE AND LOCAL HEALTH, PUB
LIBRARY FOUNDATION HEALTH LABS
SO FAR AND 3 COUNTY AND LOCAL
BUT A MAJORITY OF THEM HAVE
STAYED ON IN PUBLIC HEALTH
CAREERS WHICH IS A CRITICAL
OUTCOME, 71% HAVE STAYED IN
PUBLIC HEALTH AT SOME LEVEL AND
IF YOU LOOK AT THE FIRST 5
COHORTS OVER HALF WHICH IS
REALLY A FANTASTIC OUTCOME FOR
US.
SO THE LAST THING I WANT TO TALK
ABOUT I THINK IS THE PATHOGEN
GENOMICS CENTERS OF EXCELLENCE.
THIS IS A OPPORTUNITY FOR US TO
BUILD ON THE ACADEMIC
PARTNERSHIPS THRA WE STARTED TO
FORGE THROUGH SPHERES, EACH 1 OF
THE 5 SITES ACROSS THE U.S.
IS--I WILL SWITCH TO THE NEXT
LIED IS A PARTNERSHIP BETWEEN
THE STATE PUBLIC HEALTH
DEPARTMENT AS THE RECIPIENT AND
1 OR MORE ACADEMIC INSTITUTIONS,
THESE GROUPS HAVE INDIVIDUAL
PORTFOLIOS THAT FOCUS ON
SPECIFIC PATHOGENS AND
APPLICATIONS, THERE'S ALSO A
NUMBER OF NETWORK EFFECTS, AND
FROM THIS WE'RE TRYING TO DRIVE
NOT ONLY INNOVATION AND PUBLIC
HEALTH AND PROVIDE A READY TEST
BED FOR NEW TECHNOLOGIES AND
GNAW APPROACHES, NEW THINKING
ABOUT HOW WE USE PATHOGENOMICS,
WE TRY TO INSURE THAT WE HAVE A
GOOD ONGOING COLLABORATION
BETWEEN THE ACADEMICS AND THE
PUBLIC HEALTH PEOPLE THAT ARE
ACTUALLY IMP LEMMING THESE TYPE
OF SOLUTIONS, AND WE HAVE AN
ONGOING OPPORTUNITY FOR
WORKFORCE DEVELOPMENT AND
RECRUITMENT.
YOU KNOW BY AGAIN INCREASING
THAT REACTION SURFACE BETWEEN
ACADEME IMRA AND PUBLIC HEALTH
THIS, GIVES US A WARM BASE TO
BRING IN JUNIOR FACULTY, NEW
GRADUATES INTO PUBLIC HEALTH
CAREER ANDS EXPOSE THEM TO THE
KINDS OF PROBLEM ANDS HOPEFULLY
CONVINCE THEM TO STAY.
THIS ALSO GIVES US AN IMPORTANT
TOOL FOR RESILIENCE, THE FIRST
YEAR OR 2 YEARS OF THE PANDEMIC
AND EVEN TODAY, YOU KNOW
ACADEMIC AND CLINICAL LABS
PLAYED AN OUTSIZED ROLE IN THE
PUBLIC HEALTH RESPONSE, AND THIS
GIVES US SOME STRUCTURE, SOME
ABILITY TO ACTUALLY SURGE THAT
KIND OF CAPABILITY TO HAVE THAT
ACADEMIC PARTNERSHIP ALREADY IN
PLACE ISSUES THE AGREEMENTS
THAT'S ALREADY THERE, THE DATA
USE AND TRANSFER AGREEMENTS IN
PLACE, AND HAVE THAT FAMILIARITY
IN THE LOCAL NETWORKS READY TO
FIRE, SHOULD WE NEED THEM.
THE LAST THING I WANT TO
MENTION, IS THE AMD PLATFORM, SO
1 THINK THIS WE HAVE LEARNED IS
THE NEED FOR A CONSISTENT
ENVIRONMENT FOR BY O INFORMATIC
TOOLS.
ONE THE CHALLENGES WE FACE IN
PUBLIC HEALTH IS EACHITATE AND
PUBLIC LOCAL HEALTH DEPARTMENT,
ALL OF OUR GLOBAL PARTNER VS
DIFFERENT ACCESS TO
BIOINFORMATICS TO CLOUD
RESOURCES TO I.T., I.T.
EXPERTISE, MANY STATES AND STATE
LOCAL GOVERNMENTS HAVE PREFERRED
CLOUD VENDORS THAT DON'T
NECESSARILY ALIGN WITH THOSE IN
NEIGHBORING STATES OR YOU KNOW
THE REGION OR FEDERAL PARTNERS.
SO BY PROVIDING A CONSISTENT BY
O INFORMA, A SYSTEM WHERE THESE
TOOLS CAN RUN IN A CONSISTENT
WAY, IT ALLOWS US TO HAVE AN
ENVIRONMENT WHERE A LOT OF THE
CDC SUPPORTED ANALYSIS PLATFORM
WORK FLOWS CAN RUN CONSISTENTLY,
CAN PROVIDE ROUTINE ACCESS TO
THAT AND IDEALLY, PROVIDE AN
INTEROPERABLE ENVIRONMENT THAT
CAN WORK WITH MULTIPLE DEFINITE
DATA SYSTEMS.
THIS IS MOVING ALONG PRETTY
STEADILY, WE'VE GOT--PROBABLY
GET AN UPDATE ON THIS LATER.
I DON'T WANT TO DWELL WITH TOO
MUCH ON THIS BUT WE ARE REALLY
EXCITED ABOUT THIS.
ON THE BACK END, WE'RE ALSO
DOING A LOT OF WORK TO TRY TO
STANDARDIZE A LOT OF TOOLING AND
BIOINFORMATIC PIPELINES AND ARE
USED RETEENLY BECAUSE IDEALLY WE
WANT THEM TO BE CONTAINERIZED
PORTABLE SCALABLE, IN WAYS THAT
CAN BE BROUGHT INTO OTHER
ENVIRONMENTS AND DEPLOYED
PARTNERS AS NEEDED.
WE PUT VIRTUALLY ALL OF THE NEW
PIPELINES OUT ON GITHUB, EITHER
THE CDC GITHUB OR THE UTAH
PUBLIC HEALTH LABS, FANTASTIC
SECRET TOOL KIT DEVELOPED BY
AARON YOUNG.
A LOT OF THESE ARE DEVELOPED IN
CONTAINERIZED WAY ANDS CAN BE
RAPID LOAMACYY DEPLOYED.
WE JUST HAD A PRESENTATION ON
YESTERDAY'S SPHERES CALL FOR
STATUS, AND THIS IS OUR OPEN
T-REGGAGE AND DATABASE
SUBMISSION.
THIS A LOT OF THIS IS ON THE
TOOLING OVER THE COURSE OF THE
PANDEMIC TO TAKE THOSE MASSIVE
AMOUNTS OF COMMERCIAL SEQUENCE
DATA AND PUSH THAT INTO GISAID
AND GENBANK TO STANDARDIZE
METADAILY BASIS THEA TO RUN
QUALITY CONTROL CHECKS BUT A LOT
OF THAT IS MODULAR AND A LOT OF
IT IS DESIGNED FOR VIRAL AND
VECTERAL PATHOGENS AND SO BY
PUTTING THESE TOOLS OUT THERE,
MAKING THEM MODULAR, THEY CAN BE
USED AND REUSED, WE'RE REALLY
EXCITED ABOUT THE FUTURE OF
AVAILABILITY OF SOME OF THESE
TOOLS.
AND THEN THE LAST, THE VERY LAST
THING I WILL TALK ABOUT IS THE
QUALITY INITTIAIVE ITS WHICH
LAUNCHED IN 2019, WE'VE SINCE
REVAMPED IT BUT I THINK IT WILL
CONTINUE TO PLAY AN OUTSIDE ROLE
ESPECIALLY WITH THE REGULATORY
SCRUTINY THAT'S COMING DOWN THE
LINE EMPLOY TO DATE IT'S
RELEASED OVER A HUNDRED
DIFFERENT TOOLS, CHECK LIST AND
TEMPLATES IF YOU JUST GOOGLE NG
S QUALITY INITIATIVE, IT WILL
BRING YOU TO THIS PAGE AND
THEY'RE ALL DOWNLOADABLE AND
SEARCHABLE.
SO I WILL WRAP IT THERE.
I HAVE A FEW CRITICAL LESSONS
AND FUTURE DIRECTIONS BUT I
REALLY WOULD WELCOME SOME
QUESTIONS OR DISCUSSION IN THE
FEW MAINUTES THAT REMAIN.
APOLOGIZE FOR GOING A BIT OVER,
KYLE.
>> NO, THIS HAS BEEN GREAT.
SO, SO, INTERESTING.
I SEE A BUNCH OF QUESTIONS IN
THE BACKGROUND AND IF FOLKS HAVE
OTHERS, FEEL FREE TO SUBMIT
THEM.
LET ME SEE HERE.
I'M CURIOUS DUNCAN WHAT--I'M
SURE STANDING UP THAT FEDERAL
AND DPROABAL NETWORK, THERE WERE
A LOT OF HURDLES THAT YOU
ENCOUNTERED THAT WERE FAMILIAR
TO YOU, BUT MAYBE JUST AT A MUCH
LARGER KALE BECAUSE OF THE
UNIQUE CHALLENGES OF COVID.
I'M CURIOUS WHAT YOU WOULD
CHARACTERIZE AS THE BIGGEST
SURPRISE, MAYBE SOMETHING YOU
DIDN'T EXPECT FROM STANDING UP
THAT SORT OF INITIATIVE.
I THINK THE BIGGEST SURPRISE WAS
JUST A LEVEL OF ENTHUSIASM THAT
I SAW THROUGHOUT.
I THINK IT WAS--IT IS, WAS, IS A
UNIQUE SET OF CIRCUMSTANCES.
I THINK THERE WAS, YOU KNOW YOU
HAD MANY ACADEMIC AND CLINICAL
LABORATORIES WHOSE NORMAL
ROUTINE WORK HAD BEEN DISRUPTED,
JUST THE WILLINGNESS AND
ACTIVITY FROM A LOT OF THESE
DIFFERENT PARTNERS, BEFORE THAT
MAY HAVE HAD LIMITED EXPERIENCE
WITH PUBLIC HEALTH, SUDDENLY
ENTERING INTO THAT REALM, I
THINK THE OTHER PIECE WAS JUST
THE WELCOMENESS FROM THE PUBLIC
HEALTH COMMUNITY AT ALL LEVELS.
I THINK YOU KNOW I THINK THERE'S
A RECOGNITION THAT EVERYONE IS
ON THE SAME TEAM.
I THINK THERE WAS A WILLINGNESS
TO FIGURE OUT HOW TO NAVIGATE
THE NECESSARY PROCESS TO MAKE
THINGS WORK.
AND YOU KNOW IF MANY WAYS, IT
REALLY BECAME A REALLY EFFECTIVE
PARTNERSHIP AND I--MAYBE I
SHOULDN'T HAVE BEEN SURPRISED BY
THAT BUT I WAS SURPRISED
SOMETIMES BY THE WILLINGNESS.
>> I'M SURE A VERY WELCOME
SILVER LINING TO ALL OF THOSE
EFFORTS.
>> LET'S SEE LOOKING AT THE
QUESTIONS HERE, ARE THERE
CHALLENGES TO GETTING
BIOINFORMAT 8 HOURSS INVOFFED?
THAT CAN BE A RATE LIMITING STEP
THAT ARE KEY TO THESE SORTS OF
EFFORTS?
>> SO THE TRUTH IS WE CAN NEVER
HAVE ENOUGH BIOINFORMATICIANS,
BUT YOU KNOW DURING THE
PANDEMIC, THIS IS ESPECIALLY
TRUE BECAUSE WE, YOU KNOW WE HAD
SORT OF A CADRE OF
BIOINFORMATICIANS AT CDC AND
LOCAL HEALTH DEPARTMENTS,
WORKING INSANE HOURS TRYING TO
ANALYZE, INTERPRET AND PROVIDE
STAT REPORTS ON VARIANTS FOR A
VARIETY OF DIFFERENT AUDIENCES
AND CONSUMERS FROM YOU KNOW THE
WHITE HOUSE DOWN TO THE LOCAL
MAYOR'S OFFICE AND YOU KNOW IN
MANY CASES YOU JUST SAW PEOPLE
BURNING OUT AND NOT HAVING
ENOUGH BAND WIDTH TO SUPPORT ALL
THE NEEDS.
THAT'S A CHALLENGE WHEN YOU HAVE
A HIGHLY, HIGHLY SKILLED SKILL
SET AND HIGH DEMANDS ON IT.
THERE WERE SOME REALLY
INTERESTING OPPORTUNITIES
THROUGHOUT THAT, YOU KNOW 1 OF
THE THINGS THAT WE DID WITH ABHL
WAS TO CREATE THESE GENOMIC
INTERNSHIPS THAT WERE VIRTUAL,
THAT BASICALLY PAIRED, THEY WERE
PART-TIME WORK, THEY ALLOWED AN
EXISTING GRADUATE STUDENT OR
SOMEBODY SHANKAR HAS THE
NECESSARY BACKGROUND AND
QUALIFICATIONS TO BE PAIRED WITH
A STATE OR LOCAL HELT
ENVIRONMENT TO HELP OUT WITH THE
BIOINFORMATIC DATA ARGSINAL SIS,
DATA, QC, SUBMISSION ON THE BACK
END AND YOU KNOW, FOR US IT'S
SORT OF 2 THINGS, YOU KNOW IT
HELPED WITH THOSE INITIAL
WORKFORCE CHALLENGES AND MAKING
SURE WE HAD SKILLED HANDS
THROUGHOUT THE COUNTRY THAT
COULD BE DRAWN ON BUT IT ALL
ACTED AS A LITTLE BIT OF A
FEEDER FOR SOME OF OUR
FELLOWSHIP PROGRAMS WHICH I'M
REALLY EXCITED ABOUT.
>> YEAH, THAT'S GREAT.
ON THAT UPON --TOPIC, HAVE YOU
THOUGHT ABOUT INTEGRATE
THANKSGIVING INFO INTO COLLEGE
CURRICULUMS IN TERMS OF COLLEGE
RECRUITEES OR TRAINEES.
YOU TALK ABOUT THE NICE PROGRAMS
YOU HELP SET UP TO DRAFT THE
NEXT GENERATION OF
EPIDEMIOLOGISTS?
>> YEAH, 1 OF THE THINGS THAT
WE'RE TRYING TO DO IS INCREASE
OUR OUTREACH.
IF I LOOK OVER THE APPLICATIONS
TO OUR FELLOWSHIP PROGRAM, WHAT
I USUALLY FIND IS SOME OF THE
MOST EFFECTIVE--EFFECTIVE ADVOCA
THES THAT WE HAD ARE USUALLY
WHERE WE SEE HEATED APPLICATIONS
FROM SINGLE SCHOOLS, IT'S
USUALLY IN THE CASE WHERE WE
HAVE A VERY STRONG ADVOCATE,
THAT GOES ON LECTURES THERE OR
ADVERTISES THE PROGRAM OR
PROMOTES IT WITH STUDENTS AND
STAFF, WE'RE STARTING TO BUILD
OUT AN ALUMNI NETWORK, WE HAVE
NEW PARTNERSHIPS WITH FERGUSON,
WE CONTINUE TO HAVE PARTNERSHIPS
WITH EXISTING FELLOWSHIPS AND WE
LIKE THE LABORATORY OF
LEADERSHIP SERVICE AT CNC, LIKE
THE EIS PROGRAM, CDC, THE
CONTINUING TO BUILD THAT, BUT
YOU KNOW I THINK 1 OF THE
FUNDAMENTAL THINGS IS, YOU KNOW
WE NEED TO PUT THESE
OPPORTUNITIES IN FRONT OF MORE
PEOPLE AND NOT ONLY SORT OF THE
REGULAR SCHOOL ANDS PROGRAMS
THAT WE INTERACT WITH REGULARLY,
BUT A LOT OF THE PROGRAMS THAT
DON'T NECESSARILY GET THAT
OPPORTUNITY SO WE'RE DEFINITELY
LOOKING AT THAT.
>> GREAT, AND WITH THAT, I SEE
WE ARE AT THE TOP OF THE HOUR.
SO I WILL THANK YOU AGAIN DUNCAN
FOR YOUR TIME AND SHARING THIS
REALLY CRUCIATE LIGAMENTNIQUE
AND INSPIRING STORY AND THANKS
ALL FOR TUNING IN.