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1 January 2015 – 31 December 2015

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1 January 2015 – 31 December 2015 DST-NRF CENTRE OF EXCELLENCE ANNUAL PROGRESS REPORT Reporting Period 1 January 2015 – 31 December 2015 CONTENTS Page Executive Summary………………………………………………………………………………………………………………....….......2 Progress Report………………………………………………………………………………………………….........……5 Human Resources…………………………………………………………………………………………………….......32 Outputs…………………………………………………………………………………………………………………....……..35 Finances……………………………………………………………………………………………………………………...……53 Identification Name of Director : Professor Paul D. van Helden Names of Node Heads : Professor Valerie Mizrahi Professor Bavesh Kana Name of CoE : DST/NRF Centre of Excellence for Biomedical TB Research Abbreviated CoE Name : CBTBR Host institutions : University of Stellenbosch, University of the Witwatersrand University of Cape Town Date completed : 08/04 /2016 CBTBR Annual Progress Report: 2015 Page 1 of 53 EXECUTIVE SUMMARY 1. Financial Information (Funding of the CoE) TotalNRFfundingfor2015(entireyear)–CoEonly : R10758831 CoE-specificFundingfromHostinstitutionin2015–WITS : R230000 −UCT : R150375 −SU : R817148 FundingfromothersourcesfortheCoEin2015 : R62920884 Totalfunding : R74 877 238 Totalfundingfor2015forWitsnode: R10770183 • CoEfundingfromNRF: R2326031 • OtherfundingfromNRF: R501169, madeupasfollows: - IncentiveFunding(Kana) 1 R40000 - NRFpostdocsupplement 2 R61250 - SA-SwissJointResearchGrant 3 R399919 • FundingfromWitsandNHLS: R2535254, madeupasfollows: - 10%WitsInstitutionalCommitment R230000 - ResearchIncentiveFunding R7333 - Salaries R1496621 - NHLSResearchTrust 4 R499600 - TIA–WITSSeedFund 5 R301700 • Fundingfromothersources: R5407729, madeupasfollows: - HHMIIECSgrant 6 R1272403 - DAIDSCTUSupplement R723860 - BMGFAccelerator 7 R3186466 MRCCareerDevelopmentAward 8 R225000 Totalfundingfor2015forUCTnode: R15337253 • CoEfundingfromNRF: R1503754 • OtherfundingfromNRF: R728605 9 • FundingfromUCT(excludingsalaries ): R300000 10 • Fundingfromothersources: 11 R12804894,madeupasfollows: - MRCUnit(MMRU;Mizrahi) R1000000(1Apr2015–31Mar2016) - EUFP7(MM4TB)(Mizrahi) R781053(1Feb2015–31Jan2016) - FNIH(HIT-TB)(Mizrahi) R3224404(1Sep2014–31Aug2015) - MRCSHIPgrant(Warner) R1374561(1Jan2015–31Dec2015) - MRCFlagship1(Warner/Mizrahi) R483243(1Jan2015–31Dec2015) - HHMISIRSgrant(Mizrahi) R1130340(1Oct2014–30Sept2015) - USNationalInstitutesofHealth(Warner) R4360350(1Jan2015–31Dec2015) 12 - WellcomeTrust(Warner) R450943(1Jan2015–31Dec2015) 13 1NRFIncentiveFundingtoBDKana–Year5 2ToC.Ealand 3Year2SA-SwisstoN.DharandB.Kana 4Year1ToB.Gordhan 5ToB.Kana 6Year4toB.Kana 7Year2toB.Kana 8Year1toC.Ealand 9SA/GermanyResearchCooperationgrant(V.Mizrahi–R108,900);CompetitiveProgrammeforRatedResearchers(D.Warner –R268,990);UK/SARoyalSociety-NRFSeminar(D.Warner;R63,000);SA/ZambiaResearchCooperationgrant(D.Warner, R67,715);CommunityEngagementAward(D.Warner),R220,000). 10 TwodoctoralfellowshipsfromUCT’sCarnegieCorporation DevelopingNextGenerationAcademics program 11 Whereapplicable,externalawardsincludeindirectcosts(IDC),andZARvaluesarecalculatedbasedonlandede-rates 12 UO1andR21grantsawardedundertheNIH-SAMRCSouthAfrica-USprogramforCollaborativeBiomedicalResearch 13 PublicEngagementaward(Eh!Wozaproject) CBTBR Annual Progress Report: 2015 Page 2 of 53 Fundingfor2015forSUnode: R48769802 • CoEfundingfromNRF: R6930046 • FundingfromSU:(bestestimate): R4815000, incl.salaries,studentbursaries, excl.space,basicinfrastructure,secretary,cleaners. • Fundingfromothersources(bestestimate): R37024756 ,madeupasfollows: - MRCCentre(estimateoftheTBcomponent) R10000000(incl.salaries) - PGWC R2495 000(salariesonly) - NIHM(X)Dr-TBLatePCR R1167059 - NIHAlteredImmune-endocrinetype2diabetesR2310889 - NIHOFX R31070 - NIHExitRif R1587786 - NIHCASS R306514 - NIHOptiQ R47091 - BMGFGC6-74:Cohorts R1227639 - BMGFVirulenceofTBstrains R524473 - TANDEM(EUFP7) R1324919 - FIND R170000 - VPMClinicaltrial R3328687 - HainFluorotype R106287 - AERASClinicaltrialproject R2098399 - NRFSARchi R1119038 - MRCDrugDiscoveryforAnti-TBAgents R3399123 - MRCSHIPSATBBI R3000000 - MRCTBNext R180000 - MRCTBHart R549865 - MRCSHIPMaltTBRedox R202632 - MRCSHIP-SystemImm R552020 - DSTTANDEM R296266 - OtherNRFfunding R1000 000 2. Summary of progress against 5 KPAs (i) Research The research productivity of the CBTBR remained excellent in 2015 as evidenced by the fact that 84 articlesinpeer-reviewedjournalswerepublished,and161conferencepresentationsweremade,including 11 plenary/ keynote lectures, and numerous invited talks. Of the research articles published, 70 were in journalswithanimpactfactor(IF)>2. Progress against targets SLA 5 targets : The outputs under this KPA exceeded the SLA target ( ≥20 publicationsofwhich ≥5areinjournalswithanIF ≥2). (ii) Education and Training A total of 10 PhD students, 7 MSc students and 9 Honours students from the CBTBR graduated or completedtheirtrainingin2015.Allthesepostgraduatestudentscompleteddegreeswithintheirmaximum allowabletimeagreeduponintheSLA.OnepostdoccompletedtrainingintheUCTnodeandtookupa position at the NICD. A postdoctoral fellow at the Wits node was awarded the prestigious MRC Career Development Award andtransitioned to a fixed term contract post at Wits University in April 2015. A numberofnewpostdoctoral,PhDandMScstudentswereenrolledinthenodesoftheCBTBR,andseveral students were afforded the opportunity to work in international labs. The student breakdown according gender(59%female)andpercentageofpostdoctoralfellows(21%oftotalstudentcomplement)exceeded the SLA targets of ≥50% and ≥10%, respectively. The proportion of black students (54%) exceeded the SLA target of ≥50%. The percentage of Honours students was 10% in 2015. Progress against SLA 4 targets :Thetotalof112postgraduatestudentsassociatedwiththeCBTBRin2015greatlyexceededthe SLAtargetof ≥35. CBTBR Annual Progress Report: 2015 Page 3 of 53 (iii) Knowledge Brokerage TheCBTBRcontinuedtocontributetothedisseminationofresearchdiscoveriesthroughengagementwith thescientificcommunityatmanymeetingsandconferences,withstakeholdersinoperational/publichealth research,policymakersandinsomecases,thegeneralpublic.Wecontinuetostriveforcountry-wideand internationalpublicityinvariousmediaplatforms,suchasradioandpressandwecontinuetobeinvolved in many outreach activities, targeting school teachers and learners, and on science communication in general.Wecontinuetostriveforimprovedcommunicationwithmetropolitan,provincialandnationalhealth authorities,MédecinsSansFrontières(MSF)andNHLS.Ourinteractionwiththesestakeholderscontinues to improve. We now engage more with DoH and NHLS than before and have developed a good relationshipwithboth,suchthatourphonecallsandemailsarereceivedandrespondedto.Wecontinueto adviseSANParks,theNationalZoologicalGardens(NZG)andnowalsotheNamibianWildlifeservices,as wellassomeprivateentitieswithregardtoTBinwildlifeorcaptiveanimals.SinceJuly2015wehousedan NRF-intern science journalist to assist with this overall activity. Perhaps one of our most significant measuresofsuccessisthatProfsMizrahiandvanHeldenservedonaWHOpanel“GlobalFrameworkfor TBresearch”whichisaimedatguidingresearchendeavoursforthefuturetoassistinachievingthelofty WHOgoalofTBelimination.Participationinthispanelledtoco-authorshiponapaperpublishedinMarch 2016in PLoSMedicine .Thedirector,co-directorsandseveralteammembersoftheCBTBRalsoplayeda majorroleindiscussions,convenedbytheNationalTBThinkTankandtheSAMRC,thatwereaimedat developinganationalTBresearchstrategyduringthecourseof2015.Thisworkisongoing.Prof.Mizrahi continuedtocontributetostrategicdevelopmentoftheTBDrugAccelerator(TBDA)programoftheBill& MelindaGatesFoundationasanon-memberparticipantatTBDAmeetingsinSeattle(March)andBeijing (October). Prof Gerhard Walzl continues to be a leading member of the IMPAACT Biomarker Scientific group.Hehasattendedandledmeetingsaimedatdevelopingablueprintforsuchbiomarkers. (iv) Networking Numerousrecentfundingopportunitieshaveledtonewnetworkinginitiativesthathaveenhancedthelocal andinternationalfootprintoftheCBTBR.Thisactivityisextensive,asoutlinedinSection4ofthereport. Ourcollaborativelinksrangefrominstitional,regional,local,throughAfricatomanyinternationalconsortia and networked partners. The CBTBR regards this activity as central and vital to our activities and encouragesitasfarasispossible. (v) Service rendering Whilst not our major activity, the CBTBR continues with this activity and intends to do so in future. The CBTBR continues to assist with countrywide roll out of the GeneXpert and now provides verification standardstoover20countries,thisinnovationhasallowedthousandsofTBpatientstoaccessmolecular diagnostics. These verification standards now also fall under the GLI label, for all GLI, CDC and WHO sites. We continue to provide technical/ scientific services to the Eastern and Western Cape Provincial HealthDepartment,TygerbergHospitaland variousTBclinics.Wecontinue withourprovisionofadvice and assistance to individuals, research groups and institutions, locally (including NHLS) and abroad, committee membership and scientific review work at the institutional, regional, national and international levels.WecontinuetotestantimycobacterialsforUKZN,NWU,UWCandUCTandinternationalconsortia. Members of the CBTBR again played key advisory and participatory roles in the national and regional responses to the extensively drug-resistant (XDR) TB crisis. Assistance to SANParks, NZG, and others, such as the Namibian
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