biostudies-literatureAggarwal DMedical Research CouncilNational Institute for Health Research (NIHR)Wellcome TrustAcademy of Medical Sciences751https://www.ebi.ac.uk/biostudies/studies/S-EPMC8826310biostudies-literatureUnknown13(1)Understanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infeNature communicationsGenomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission.PMC8826310222903/Z/21/Z207498/Z/17/ZMR/P008801/1MR/S00291X/1AMS-CSF4-Torok206298/B/17/ZACF-2020-14-007MC_UU_00002/11MC_PC_19026MC_PC_19027MC_UU_12014/12204911/Z/16/ZDabrera GSmith CPMacIntyre-Cockett GHarper KLPaterson SSouthgate JStark RMadona PGroves DCSluga GMichelsen MLMaclean AHarris KACarlile MLyons RACotic MLoose MWHowe RLetchford LStarinskij IHamilton WLSang FFatseas TEdgeworth JSwindells EMargolis BO'Grady JIturriza-Gomara MRowan AWilliman JSmith DLStockton JMbisa TRussell MBellis KLRambaut AYeats CAStorey NPlatt SKitchen CUnderwood APYoung JScarlett GPKraemer MUGPartridge DGPoppitt SVipond IBLangford CFMachin NWShankar GEccles RWhite PChappell JGFreeman TMMichell SLBird PWesthorpe APMactavous LJesudason NGCurran TEvans JMBirchley ACumley NGallagher EParmar SCoombes JSato ANichols JBishop CHassan-Ibrahim MOThornton APage AJCraine NCowell ALe-Viet TValletta SHesketh ARWaugh SKnight BABlacow RBewshea CMAfifi SGoodwin SPaul HVasylyeva TIWeekes MPDavis TSaluja TMahanama AIKEltringham GColl FHolden MTGDuckworth NBoyd OSilveira SAbell CJackson DKNomikou KRaviprakash VMoll RJNelson ANeely AMcKenna JPRushton SBronner IFBall JCorden SZamudio MENelson CTucker RMSaeed KMenegazzo MNelson RBridgewater HEGilbert LLucaci AOMills JAtkinson LMyers RKnapton JParker MDKahkeshi MBAriani CVOrton AKhakh MGifford LMcManus GMGrammatopoulos DSing RSambles CMHutchings SCaspersz MPoplawski RVattipally SQuick JJohnson KJohnson NThomson ECJohnson RSheriff NBradshaw DBarton EWilson HDFarr BWGallis MMori MLiddell KGallagher MDHarrison JWJordan SDorman MJPusok Mde Oliveira Martins LChurcher CMGoncalves SJeffries ARSearle PKenyon AJohnson DGransden LForrest SKeeley AJWarne BWyles MLedesma JHogsden WBlane BWhitehead MDrury EAsamaphan PMungovan DPandey SMoles-Garcia EHartman HGregory RMerrick IManesis NCharalampous TEyre DMayhew MMcCluggage KAlam MTAhmad SSYSamaraweera BShepherd JGLindsey BBCeaser MAmato RCarmichael SNChapman MRCrowcroft JDurham JHeaney JLacy EDarby ACTorok MEShah DBourgeois YAlcolea-Medina AWaddell ILouka SFWhiteley MBrown CARajatileka SBaxter LMathieson NFearn CMakunin ARaza MFarbos AWills MVinnell MDewar RRowe WFallon KNikitina KGatica-Wilcox BBonsall DBassett ARDavidson RKWeale GLo SCurran MDDyer RJohnston IDervisevic SCook KLister MMBoYes JRuis CCasey ALloyd ADent HWilson-Davies EShaw AMason JGeorgiou CSignell AWNicholls SEldirdiri SFaulkner KPacchiarini NSchaefer UBradley DTSmollett KLHelmer TMeadows LJackson KAAwan ARBeckett AHMerrill TVMollett GTong LBosworth AMcMurray CGourtovaia MCox AWitele EHalstead FKaramani ACheng JKJReynolds NAngelis DGulliver HBeale MAHowes RWilliams RJKay SFleming VMRankin JBaker PBurton-Fanning SAttwood SWDowning FClarke RHaque THopes RElliott SLeong CMcKerr CPayne BALudden CTovar-Corona JMWyllie SLensing SVWise EBresner CEnsell LChand MGlew RTaylor-Joyce GVernet GBreen CCambridge Covid-19 testing CentreJahun ASNsonwu OFrancois SVolz EMKumziene-SummerhaYes SMunn RHannan SRainbow LAngyal ATodd JAHarrison EMHigginson EESinger JBSymmonds APlimmer ARamsay MMarchetti FDebebe JQuinnell NPeto TJeremiah SFeltwell TLivett RCrook DBarrett JPercival BHarrison ITrebes ABrierley CFerris MCronin MChauhan AJChalker VBeggs AHowson-Wells HCYew WCMaes MBonfield JSloan TJHeyburn DGlover MGoodfellow IGKay GLSmith LFina LRudder SRobinson TIMeader EJStanley RAigrain LWilson RESmith NChatterton WPrieto JARadecki ASmith WPerry MLambson OMolnar ZOliver KFisher CLFenton MLPatel ABedford LIllingworth CJAhmadi-Assalemi GCrawford LAcheson EMahungu TWOsman HWilliams DTaylor SJohn MMcNally ATaylor PAlikhan NFMalone CSBibby DJames KWright VWilliams CTolhurst JJames LHancock DKermack LMWright GStanton TDHilborne SWright JAuckland CMookerjee SPatel MGreenaway JLoveson KFWright EBetancor GLynch JTaha YHosaja AShah RNHall GMcCann CMJamrozy DGutierrez BWatkins EPatel VMirza JTemperton BDouthwaite JMair DFoulser LRagonnet-Cronin MBoswell TBrown JRWatkins JSheldrake ZRatcliffe LDougan GMarchbank AWilliams TMather AEWilliams LATempleton KETwohig KAWilliams RBuck DGoudarzi SGeorgana IHosmillo MJones HJones CFeather TNebbia GNunez RTMRoy SGirgis STHilvers ELiddle Jda Silva Filipe Adu Plessis LBradley AGreen AO'Toole AMaxwell PSnell LBPearson CPark NRO'Toole EHubb JShirley LWinster JPymont HMMetaxaki MIzuagbe RWeldon DTrotter AJPinckert MBeaver CHill VHughes GJXu-McCrae LAshcroft FHollamby VGreatorex JFraser CFrost LRWarwick-Dugdale JCerda ACUniversity of Cambridge Asymptomatic COVID-19 Screening Programme ConsortiumMcClure PCManley RWyatt TGroves NLi KKEnright JDanaei DHunt MBetteridge ELewis KGuest MNascimento FFCarden HCOVID-19 Genomics UK (COG-UK) ConsortiumKeen MWebster HJOrton RJEvans CLiggett SWantoch MGupta RKAllara EManso CTurtle LAggarwal DLeonard SJones KJones RJones SRobson SCChaudhry AScott GKidd SRajan DScott CHolgate JEllard SRooke SGill HKAranday-Cortes ECarabelli AMHoensch SJackson CDanesh JHale ADDadrah AChaudhry YGaskin ATsoleridis TBeer RRichter AUnnikrishnan MLevene NWalsh SBayzid NMuir PGolubchik TVignoles AHart JWatts JMoore JAanensen DMMoore NParlikad ACortes NGunson RNLeslie IMoore CGeorge RPCottrell SCormie CMoses SCollins JThompson TDavies AClark GDhada MMartincorena INiebel MOIrish-Tavares DWilson KLeek DMiah SSmith KSOtt SZhang PWilliams CARidgman TWhitwham AYoung GRHughes MHughes RConstantinidou CLehner PKuenzi FO'Brien SCogger BJKane LHughes JEdwards SConnor DSamworth RMurphy ELevett LJAndersson MDavies RMcCarthy SGlaysher SBlakey VRaub GClark RBreuer JFairley DJBashton MAsh ABest ATynan JTaylor BEWWorkman CNickbakhsh SMcFarlane DGibbs KTonkin-Hill GLawniczak MMcNulty CGoodall RHenderson RLee DTang JHartley JAWorkman TMcHugh MPJones DRMatheson NWilliamson KAAbudahab KMatthews SMozdzen BPrice JCoupland LJustice AAdams AMaksimovic JRaghwani JAdams HBatra RRandell PAConnor TRHaldenby STBolt FBicknell KHiscox JAPrice AJones CRLackenby AKoshy CWierzbicki CBrown PESridhar SFieldman TGalai KZarebski AEStonehouse SWang DFlaviani FKeatley JPBraithwaite VRey SKristiansen MIllingworth CBrown CBrooks EBerry LChapman MHSLoman NJImpey RHolmes Ade Silva TIRees SSamtani VBerry SPadgett DHolmes CLowe HSiveroni IFreeling ASimpson DAJannoo RLee JCDGraham CVamos EERobertson DLGraham LLowe HLGemmell MBroos AAsad HKwiatkowski DShaaban SAydin ABrown NMGeidelberg LMegram OPrestwood LEmanuela PSivaprakasam VMcGuigan SWastenge ESheridan LQuail MAPacker SMonaghan LEssex SHadjirin NFde Cesare MBaker DJJorgensen DSpellman KRedshaw NMMaxwell PHTaylor GPBonner SAlderton ADahal AEllaby NBull MSillitoe JPalmer SHolmes NJahun ACampbell SPeacock SJFuller WGoodfellow IPybus OGThurston SAJStudholme DJPinckert MLBucca GBalcazar CEGreen LRFuller SPuethe CWillingham IMorgan SParsons PJJoseph AMatheson NJRobinson EMacfarlane-Smith LRMasoli JAHMorgan MBrown RDias JfalseGenomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission.Understanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infe2022-01-01T00:00:00Z2022 Feb2025-04-18T16:34:50.14Z2025-04-07T03:50:55.768ZS-EPMC88263103513606810.1038/s41467-021-27942-w