estimating the infection fatality risk of covid-19 in …...2020/06/27 · 50 to case and mortality...

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EstimatingtheinfectionfatalityriskofCOVID-19inNewYorkCity,March1–May16,20201

WanYang,1*SasikiranKandula,2MaryHuynh,3SharonK.Greene,4GretchenVanWye,3Wenhui2

Li,3HiuTaiChan,3EmilyMcGibbon,4AliceYeung,4DonaldOlson,5AnneFine,4JeffreyShaman23 1DepartmentofEpidemiology,MailmanSchoolofPublicHealth,ColumbiaUniversity;4

2DepartmentofEnvironmentalHealthSciences,MailmanSchoolofPublicHealth,Columbia5

University;3BureauofVitalStatistics,NewYorkCityDepartmentofHealthandMentalHygiene;6 4BureauofCommunicableDisease,NewYorkCityDepartmentofHealthandMentalHygiene;7

5BureauofEquitableHealthSystems,NewYorkCityDepartmentofHealthandMentalHygiene.8

*correspondenceto:[email protected](WY)9

10

Abstract11

DuringMarch1-May16,2020,191,392laboratory-confirmedCOVID-19caseswerediagnosed12

andreportedand20,141confirmedandprobableCOVID-19deathsoccurredamongNewYork13

City(NYC)residents.Weappliedanetworkmodel-inferencesystemdevelopedtosupportthe14

City'spandemicresponsetoestimateunderlyingSARS-CoV-2infectionrates.Basedonthese15

estimates,wefurtherestimatedtheinfectionfatalityrisk(IFR)for5agegroups(i.e.<25,25-44,16

45-64,65-74,and75+years)andallagesoverall,duringMarch1–May16,2020.Weestimated17

anoverallIFRof1.45%(95%CredibleInterval:1.09-1.87%)inNYC.Inparticular,weeklyIFRwas18

estimatedashighas6.1%for65-74year-oldsand17.0%for75+year-olds.Theseresultsare19

basedonmorecompleteascertainmentofCOVID-19-relateddeathsinNYCandthuslikely20

moreaccuratelyreflectthetrue,higherburdenofdeathduetoCOVID-19thanpreviously21

reportedelsewhere.Itisthuscrucialthatofficialsaccountforandcloselymonitortheinfection22

rateandpopulationhealthoutcomesandenactpromptpublichealthresponsesaccordinglyas23

thepandemicunfolds.24

Keywords:COVID-19;infectionfatalityrisk;age-specific;reportingrate;NewYorkCity25

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Introduction27

ThenovelcoronavirusSARS-CoV-2emergedinlate2019inChinaandsubsequentlyspreadto28

200+othercountries.AsofJune26,2020,therewereover9.47millionreportedCOVID-1929

All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprintthis version posted June 29, 2020. ; https://doi.org/10.1101/2020.06.27.20141689doi: medRxiv preprint

NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice.

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casesandover484.2thousanddeathsworldwide.1Asthepandemiccontinuestounfoldand30

populationsinmanyplacesworldwidelargelyremainsusceptible,understandingtheseverity,31

inparticular,theinfectionfatalityrisk(IFR),iscrucialforgaugingthefullimpactofCOVID-19in32

thecomingmonthsoryears.However,estimatingtheIFRofCOVID-19ischallengingduetothe33

largenumberofundocumentedinfections,fluctuatingcasedetectionrates,andinconsistent34

reportingoffatalities.Further,theIFRofCOVID-19couldvarybylocation,givendifferencesin35

demographics,healthcaresystems,andsocialconstruct(e.g.,intergenerationalhouseholdsare36

thenorminsomesocietieswhereasolderadultscommonlyresideandcongregateinlong-term37

careandadultcarefacilitiesinothers).MostIFRestimatesthusfarhavecomefromdata38

recordedinChina,theDiamondPrincesscruiseship,andFrance.2-5YettheIFRintheUnited39

States—thecountrycurrentlyreportingthelargestnumberofcases—remainsunclear.40

41

NewYorkCity(NYC)reporteditsfirstcaseonMarch1,2020,inatraveler,andquickly42

becametheepicenterintheUnitedStates.ByMay16,2020,therewere191,392diagnosed43

casesand20,131deathsreportedinNYC(Table1).Duringthepandemic,theNYCDepartment44

ofHealthandMentalHygiene(DOHMH)andtheMailmanSchoolofPublicHealthatColumbia45

Universityhavebeencollaboratingingeneratingreal-timemodelprojectionsinsupportofthe46

City'spandemicresponse.Ourlatestmodel-inferencesystemusesanetworkmodeltosimulate47

SARS-CoV-2transmissionintheCity's42UnitedHospitalFundneighborhoods.6Themodelis48

runinconjunctionwiththeEnsembleAdjustmentKalmanFilter(EAKF)7andfitsimultaneously49

tocaseandmortalitydataforeachofthe42neighborhoodswhileaccountingforunder-50

detection,delayfrominfectiontocasereportinganddeath,andchanginginterventions(e.g.,51

socialdistancing).Inthisstudy,weapplythisnetworkmodel-inferencesystemtoestimatethe52

IFRfor5agegroups(i.e.<25,25-44,45-64,65-74,and75+years)andallagesoverall,from53

March1toMay16,2020.Intheprocess,wealsoestimatereportingrates—i.e.thefractionof54

infectionsdocumentedasconfirmedcases—andthecumulativeinfectionratebyMay16,2020.55

56

Methods57

Data58



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Laboratory-confirmedCOVID-19casesreportedtotheNYCDOHMHwereaggregatedbyweek59

ofdiagnosisandagegroup(<1,1-4,5-14,15-24,25-44,45-64,65-74,and75+years)foreachof60

the42UnitedHospitalFundneighborhoods6inNYC,accordingtothepatient’sresidential61

addressattimeofreport.Themortalitydata,fromdeathsregisteredandanalyzedbytheNYC62

DOHMH,combinedconfirmedandprobableCOVID-19-associateddeaths.ConfirmedCOVID-19-63

associateddeathsweredefinedasthoseoccurringinpersonswithlaboratory-confirmedSARS-64

CoV-2infection;andprobableCOVID-19deathsweredefinedasthosewithCOVID-19,SARS-65

CoV-2,orasimilartermlistedonthedeathcertificateasanimmediate,underlying,or66

contributingcauseofdeathbutdidnothavelaboratory-confirmationofCOVID-19.8Dueto67

privacyconcerns,mortalitydatawereaggregatedto5coarseragegroups(<18,18-44,45-64,68

65-74,and75+years)foreachneighborhoodbyweekofdeath.Tomatchwiththeagegrouping69

forcasedata,weusedthecitywidefractionofdeathsoccurringineachofthefivefinerage70

groups(i.e.<1,1-4,5-14,15-24,25-44)toapportiondeathsinthe<18and18-44yearage71

categories.Forthisstudy,caseandmortalitydatawerebothretrievedonMay22,2020.72

73

Themobilitydata,usedtomodelchangesinCOVID-19transmissionrateduetopublic74

healthinterventionsimplementedduringthepandemic(e.g.,socialdistancing),camefrom75

SafeGraph9,10andcontainedcountsofvisitorstolocationsineachzipcodebasedonmobile76

devicelocations.Thereleaseddatawereanonymizedandaggregatedinweeklyintervals.We77

spatiallyaggregatedthesedatatotheneighborhoodlevel.78

79

Thisstudywasclassifiedaspublichealthsurveillanceandexemptfromethicalreview80

andinformedconsentbytheInstitutionalReviewBoardsofbothColumbiaUniversityandNYC81

DOHMH.82

83

Networktransmissionmodel84

Thenetworkmodelsimulatedintra-andinterneighborhoodtransmissionofCOVID-19and85

assumedsusceptible-exposed-infectious-removed(SEIR)dynamics,perthefollowingequations:86



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!"#!$ = −"# '()*#+,-#(.(/0(

(123

(14!5#!$ = "# '()*#+,-#(.(/0(

(123

(14− 5#6

!.#!$ =

5#6 −

.#7

!8#!$ =

.#7

87

88

whereSi,Ei,Ii,Ri,andNiarethenumbersofsusceptible,exposed(butnotyetinfectious),89

infectious,andremoved(eitherrecoveredordeceased)individualsandthetotalpopulation,90

respectively,fromagivenagegroup(describedbelow)inneighborhoodi.)*#+,isthecitywide91

transmissionrate,whichincorporatedseasonalvariationasobservedforOC43,abeta-92

coronavirusinhumansfromthesamegenusasSARS-CoV-2.11Toallowdifferentialtransmission93

ineachneighborhood,weincludedamultiplicativefactor,bi,toscaleneighborhoodlocal94

transmissionrates.ZandDarethelatencyandinfectiousperiods,respectively(TableS1).95

96

Thematrix[cij]representschangesincontactratesovertimeandconnectivityamong97

neighborhoodsandwascomputedbasedonmobilitydata.Briefly,changesincontactrates98

(eitherintraorinterneighborhoods)forweek-twerecomputedasaratioofthenumberof99

visitorsduringweek-ttothatduringtheweekofMarch1,2020(thefirstweekofthepandemic100

inNYCwhentherewerenointerventionsinplace),andfurtherscaledbyamultiplicativefactor101

m1;m1wasestimatedalongwithotherparameters.Tocomputetheconnectivityamongthe102

neighborhoods,wefirstdividedtheinter-neighborhoodmobilitybythelocalmobility(thisgave103

arelativemeasureofconnectivity;e.g.,iftwoneighborhoodsarehighlyconnectedwithlotsof104

individualstravelingbetweenthem,inter-neighborhoodmobilitywouldbecloserto1and105

muchlowerthan1otherwise);wethenscaledtheserelativeratesbyamultiplicativefactorm2,106

whichwasalsoestimatedalongwithotherparameters.107

108

Observationmodel109



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Toaccountfordelaysindiagnosisandreporting,weincludedatime-from-infectious-to-case-110

reporting(i.e.,diagnosis)lag,drawnfromagammadistributionwithameanofTmandstandard111

deviation(SD)ofTsddays.Toaccountforunder-detection,weincludedacasereportingrate(r),112

i.e.thefractionofinfections(includingsubclinicalorasymptomaticinfections)reportedas113

cases.Tocomputethemodel-simulatednumberofnewcasesperweek,wemultipliedthe114

model-simulatednumberofinfectionsperday(includingthosefromthepreviousweeks)bythe115

reportingrate,andfurtherdistributedthesesimulatedcasesintimeperthedistributionof116

time-from-infectious-to-case-reporting.Wethenaggregatedthedailylagged,reportedcasesto117

weeklytotalsformodelinference(seebelow).Similarly,tocomputethemodel-simulated118

deathsperweek,wemultipliedthesimulated-infectionsbytheIFRandthendistributedthese119

simulateddeathsintimeperthedistributionoftime-from-infectious-to-death,andaggregated120

thesedailynumberstoweeklytotals.Foreachweek,thereportingrate(r),themean(Tm)and121

standarddeviation(Tsd)oftime-from-infectious-case-reporting,andtheIFRwereestimated122

basedonweeklycaseandmortalitydata.Thedistributionoftime-from-diagnosis-to-deathwas123

basedonobservationsofn=15,686COVID-19confirmeddeathsinNYC(gammadistribution124

withmean=9.36daysandSD=9.76days;TableS1).125

126

Parameterestimation127

Toestimatemodelparameters(bi,βcity,Z,D,m1,m2,Tm,Tsd,r,andIFR,fori=1,…,42)andstate128

variables(Si,Ei,andIi,fori=1,…,42)foreachweek,weranthenetwork-modelstochastically129

withadailytimestepinconjunctionwiththeEAKFandfittoweeklycaseandmortalitydata130

fromtheweekstartingMarch1totheweekendingMay16,2020.TheEAKFusesanensemble131

ofmodelrealizations(n=500here),eachwithinitialparametersandvariablesrandomlydrawn132

fromapriorrange(seeTableS1).Aftermodelinitialization,themodelensemblewasintegrated133

forwardintimeforaweektocomputethemodel-simulatednumberofcasesanddeathsfor134

thatweek;thesepriorestimateswerethencombinedwiththeobservedcasesanddeathsfor135

thesameweektocomputetheposteriorperBayes'theorem.7Theposteriordistributionof136

eachmodelparameter/variablewasupdatedforthatweekatthesametime.7Thisparameter137

estimationprocesswasdoneseparatelyforeachoftheeightagegroups(i.e.<1,1-4,…,and138



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75+).Toaccountforstochasticityinmodelinitiation,werantheparameterestimationprocess139

independently10times.Resultsforeachagegroupwerecombinedfromthese10runs(each140

with500realizations).TocombineestimatesofreportingrateandIFRfor<25year-oldsorall141

agesoverall,weweightedtheage-groupspecificestimatesbythefractionofestimated142

infectionsfromeachrelatedgroup.143

144

Results145

Themodel-inferencesystemwasabletorecreatethecaseandmortalitytimeseriesforeach146

agegroupandallagesoverall(Fig.1).Formostagegroups,confirmedcasespeakedduringthe147

weekofMarch29andthemortalityratepeakedaboutoneweeklaterthanthecaserate,due148

tothetime-lagfromsevereinfectiontodeath(Fig.1).149

150

Therewere,however,substantialunder-detectionofinfections,variationsbyagegroup,151

andfluctuationsofcasereportingratesovertime,inpartduetochangingtestingcriteria(e.g.,152

testingwasrestrictedtoseverelyillpatientsintheearlyphaseduetomaterialshortagesin153

testingequipmentandpersonalprotectiveequipment).Theestimatedreportingrateforall154

agesoverallstartedatalowlevelof2.3%[median;95%credibleinterval(CrI):0.4–4.5%;same155

below]intheweekofMarch1;itincreasedto21.4%(95%CrI:14.4–31.3%)intheweekof156

March15andstayedatsimilarlevelsafterwards(Fig2F).Theestimatedreportingratewas157

highestforthetwooldestagegroupsandsubstantiallylowerforyoungeragegroups(Fig2D158

andEvs.Fig2A-C).Duringthelastweekofthisstudy(i.e.,May10,2020),weestimatedthat159

25.9%(95%CrI:15.1–41.8%)ofinfectionsamong65-74year-oldsand34.2%(95%CrI:23.0–160

49.9%)among75+year-oldswerereported;incomparison,only10.6%(95%CrI:7.4–17.7%)of161

infectionsamong<25year-oldsand16.9%(95%CrI:13.1–26.8%)among25-44year-oldswere162

reported.163

164

Afteraccountingforthecasereportingrate,theepidemicpeakfornewinfections165

occurredoneweeksoonerduringtheweekofMarch22,2020for<45year-oldsandallages166

combined(Fig2A-BandF).Thiswascoincidentwiththetimingofpublichealthinterventionsin167



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NYC–publicschoolsinNYCwereclosedonMarch16,2020andacitywidestay-at-homeorder168

wasimposedstartingtheweekofMarch22,2020.12Talliedovertheentirestudyperiod,the169

estimatedoverallcumulativeinfectionratewas15.8%(95%CrI:11.4–24.4%)byMay16,2020.170

However,theestimatedcumulativeinfectionratevariedsubstantiallybyagegroup.171

Specifically,25-44and45-64year-oldshadthehighestcumulativeinfectionrates,at20.1%172

(95%CrI:14.4–30.0%)and20.7%(95%CrI:15.7–28.0%),respectively;65-74and75+year-olds173

hadthesecondhighestcumulativeinfectionrates,at14.9%(95%CrI:11.2–22.8%)and12.9%174

(95%CrI:9.9–19.9%);and<25year-oldshadthelowestcumulativeinfectionrate(8.0%;95%175

CrI:5.1–16.7%).Ofnote,theseestimates,albeitwithlargeuncertainties,areinlinewith176

reportedmeasuresfromserologysurveys(e.g.,19.9%positiveinNYC,asofMay1,2020,likely177

fromtestingof25-64year-olds13,14).Inaddition,thespatialvariationestimatedbyourmodel-178

inferencesystem15wasinlinewithreportedmeasures(i.e.,highestintheBronxandlowestin179

Manhattan13,14).Thisconsistencywithindependentserologysurveydataprovidessome180

independentvalidationofourmodelestimates.181

182

DuringMarch1-May16,2020,atotalof20,141COVID-19deaths(15,723confirmed183

and4,418probable)and191,392COVID-confirmedcaseswerereportedinNYC.Thecrude184

confirmedcasefatalityriskwasthus8.22%.Afteraccountingforchangingcasereportingrates185

andexcludingthefirstthreeweeks(i.e.,March1-21,2020)withzeroorfewreporteddeaths186

forwhichmodelestimateswerelessaccurate,weestimatethattheoverallIFR,includingboth187

confirmedandprobabledeaths,was1.45%(95%CrI:1.09–1.87%)duringMarch22–May16,188

2020.189

190

Examiningestimatesbyagegroup,estimatedIFRwaslowestinyoungagegroups.The191

averageIFRwas0.011%(95%CrI:0.005–0.016%)for<25year-olds,increasedby~10foldto192

0.12%(95%CrI:0.077–0.15%)for25-44year-olds,andbyanother7foldto0.94%(95%CrI:193

0.74–1.21%)for45-64year-olds(Fig.3A-C).TheseestimatesweresimilartoIFRsreportedfor194

Chinaforcorrespondingagegroups.3However,theestimatedIFRforthetwooldestage195

groupswasmuchhigherthantheyoungeragegroupsandabouttwiceashighasratesreported196



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fortheseagegroupsinChina.3,4TheaverageIFRwas4.67%(95%CrI:3.21–6.66%)for65-74197

year-oldsand13.83%(95%CrI:9.65–17.78%)for75+year-olds.Inaddition,theestimatedIFR198

fluctuatedsubstantiallyovertimeforthesetwoelderlygroups.For65-74year-olds,estimated199

IFRwas6.10%(95%CrI:4.90–7.57%)duringtheweekofApril5,2020butdecreasedto3.79%200

(95%CrI:1.68–6.90%)duringtheweekofMay10,2020(Fig3D).For75+year-olds,IFRwas201

estimatedtobe16.99%(95%CrI:13.15–20.11%)duringtheweekofApril5,2020but202

decreasedto9.77%(95%CrI:4.53–14.81%)duringtheweekofMay10,2020(Fig3F).203

204

Discussion205

InlightofthelargeuncertaintiesinIFRsforCOVID-19duetounder-ascertainmentofcases,we206

haveusedamodel-inferencesystem,developedtosupportthepandemicresponseinNYC,to207

estimatelocalIFRs.DuringMarch1–May16,2020,NYCrecordedthelargestnumbersof208

COVID-19casesanddeathsintheUSandperhapsworldwide.Despitepublichealtheffortsto209

slowthepandemic,e.g.bysocialdistancing,andtorampuphealthcarecapacity,over20,000210

liveswerelostfromCOVID-19inashortspanoftwomonths.Basedonthislargenumberof211

deaths,theestimatedoverallIFRwas1.45%inNYC.Thisestimateincludedbothconfirmedand212

probableCOVIDdeaths.IfonlyCOVIDconfirmeddeathswereincluded,giventhat78.0%of213

deathsamongthetotalwerelaboratory-confirmed,theestimatedoverallIFRwouldbearound214

1.1%.Bothestimateswerehigherthanpreviouslyreportedforelsewhere(e.g.,about0.7%in215

bothChina3andFrance5).Importantly,NYChasnosologistswhoreviewalldeathcertificates216

andrecorddeathsintoaunifiedelectronicreportingsystemrapidly.Thismortalitysurveillance217

infrastructureandenhancednosologythusallowmorerapidandcompletedeathreportingin218

NYC.Assuch,ourestimatesherelikelymoreaccuratelyreflecttheunderlyingfatalityriskof219

COVID-19infection.Further,giventhelikelystrongerpublichealthinfrastructureand220

healthcaresystemsinNYCthanmanyotherplaces,16thehigherIFRestimatedheresuggests221

thatmortalityriskfromCOVID-19maybehigherintheUnitedStatesandlikelyothercountries222

aswellthanpreviouslyreported.Ofnote,despitethelargesurgeincasesandhospitalizations,223

throughquickexpansionofhealthcaresystems,mosthospitalsinNYCwereabletomeet224

patientcaredemandduringthetwo-monthperiod.AsmanyjurisdictionsintheUnitedStates225



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areconsideringre-openingaftermonthsofsocialdistancing,itiscrucialthatofficialsaccount226

forandcloselymonitortheinfectionrateandhealthoutcomesincludinghospitalizationsand227

mortalityandtakepromptpublichealthresponsesaccordingly.228

229

WhiletheIFRestimatedherewassimilartothosepreviouslyreportedelsewherefor230

youngeragegroups,wefoundthatIFRsforindividuals65yearsandolderinNYCwereabout231

twiceashighaspriorreports.3ThesehigherIFRsmaybeinpartduetodifferencesin232

populationcharacteristics,inparticular,theprevalenceofunderlyingmedicalconditionssuch233

asdiabetesmellitus,chroniclungdisease,andcardiovasculardisease.17,18Regardless,234

estimatedweeklyIFRwasashighas6.1%for65-74year-oldsand17.0%for75+year-olds.235

ThesedireestimateshighlighttheseverityofCOVID-19inelderlypopulationsandthe236

importanceofinfectionpreventionincongregatesettings.Thus,earlydetectionandadherence237

toinfectioncontrolguidanceinlong-termcareandadultcarefacilitiesshouldbeapriorityfor238

COVID-19responseasthepandemiccontinuestounfold.239

240

Inthisstudy,weincorporatedmultipledatasources,includingage-grouped,spatially241

resolvedcaseandmortalitydataaswellasmobilitydata,tocalibrateourmodel-inference242

system.Ofnote,thetimingoftheCOVID-19pandemicvariedsubstantiallyamongNYC243

neighborhoods.Forinstance,peakmortalityratesoccurredupto4weeksapartamongthe42244

neighborhoods.Fittingthemodel-inferencesystemsimultaneouslytothesediversecaseand245

mortalitytimeseriesthusenabledbetterconstraintofkeymodelparameters(e.g.,case246

reportingrateandIFR).However,wenotethereremainlargeuncertaintiesinmodelestimates.247

AfullassessmentofCOVID-19severitywillrequirecomprehensiveserologysurveysofthe248

populationbyagegroupandneighborhood,giventhelargeheterogeneityofinfectionrates249

acrosspopulationsegmentsandspace.Inaddition,weonlyincludeddeathsthatwerelab-250

confirmedorexplicitlycodedasrelatedtoCOVID-19.Arecentstudyreportedthatexcess251

deathsinNYCduringaboutthesameperiodcouldbemorethan24,000.8Further,recent252

studieshavereportedseveresequelaeofCOVID-19inchildren,i.e.Multi-systemInflammatory253



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SyndromeinChildren.Thus,itisimportanttomonitorhealthoutcomesinyoungeragegroups254

post-infectionasthepandemicunfolds,despitethelowIFRsnotedtodate.255

256

Acknowledgments:257

ThisstudywassupportedbytheNationalInstituteofAllergyandInfectiousDiseases258

(AI145883),theNationalScienceFoundationRapidResponseResearchProgram(RAPID;259

2027369),andtheNYCDOHMH.WethanktheNYCDOHMHBureauofVitalStatisticsteamand260

staffmembersintheNYCDOHMHIncidentCommandSystemSurveillanceandEpidemiology261

Sectionfordatamanagement.WethankMirandaS.MooreatNYCDOHMH,whowroteand262

maintainedthecodetogenerateweeklyextractsofCOVID-19casedataforprovisionto263

ColumbiaUniversityunderadatauseagreement.WethankJaimieShaffatNYCDOHMHand264

HelenAlesburyandKateKleinattheOfficeofChiefMedicalExamineroftheCityofNewYork265

forinitiatingandcoordinatingdiscussionsonmodelingCOVID-19mortalityinNYC.Wealso266

thankColumbiaUniversityMailmanSchoolofPublicHealthforhighperformancecomputing267

andSafeGraph(safegraph.com)forprovidingthemobilitydatausedinthisstudy.268

269

ConflictofInterest:270

JSandColumbiaUniversitydisclosepartialownershipofSKAnalytics.JSdisclosesconsultingfor271

BNI.Otherauthorsdeclarenoconflictofinterest.272

273

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yang/COLUMBIA-COVID19-PROJECTIONS-FOR-316

NYC/blob/master/summary_nyc.projection200316_CU_updated.pdf.317

12. NewYorkStateDepartmentofHealth.NewYorkstateonpause2020[cited2020318

5/16/2020].Availablefrom:https://coronavirus.health.ny.gov/new-york-state-pause.319

13. www.governor.ny.gov.AmidongoingCOVID-19pandemic,governorcuomoannounces320

resultsofcompletedantibodytestingstudyof15,000peopleshowing12.3percentof321

populationhasCOVID-19antibodies2020[updatedMAY2,2020;cited20205/12/2020].322

Availablefrom:https://www.governor.ny.gov/news/amid-ongoing-covid-19-pandemic-323

governor-cuomo-announces-results-completed-antibody-testing.324

14. GoodmanJD,RothfeldM.1in5newyorkersmayhavehadcovid-19,antibodytests325

suggest2020[updated4/23/2020;cited20205/12/2020].Availablefrom:326

https://www.nytimes.com/2020/04/23/nyregion/coronavirus-antibodies-test-ny.html.327

15. YangW,KandulaS,ShamanJ.Projectionsofcovid19epidemicoutcomesandhealthcare328

demandsforNewYorkCity(NYC)2020[cited20205/12/2020].Availablefrom:329

https://github.com/wan-yang/COLUMBIA-COVID19-PROJECTIONS-FOR-NYC.330

16. Medbelle.Besthospitalcitiesranking20192019.Availablefrom:331

https://www.medbelle.com/best-hospital-cities-usa.332

17. ClarkA,JitM,Warren-GashC,GuthrieB,WangHH,MercerSW,SandersonC,McKeeM,333

TroegerC,OngKI,ChecchiF,PerelP,JosephS,GibbsHP,BanerjeeA,EggoRM.Howmany334

areatincreasedriskofsevereCOVID-19disease?Rapidglobal,regionalandnational335

estimatesfor2020.medRxiv.2020:2020.04.18.20064774.336

18. CDCCOVID-19ResponseTeam.Preliminaryestimatesoftheprevalenceofselected337

underlyinghealthconditionsamongpatientswithcoronavirusdisease2019—United338



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States,february12–march28,2020.MorbidityandMortalityWeeklyReport.339

2020;69(13):382.340

341



https://doi.org/10.1101/2020.06.27.20141689

14

Table1.Summaryestimates.CasesanddeathswerereportedduringMarch1–May16,2020.

Crudecasefatalityrisk(CFR)wascomputedastheproportionofpersonswithconfirmed

COVID-19illnesswhodied.Cumulativeinfectionrates,median(95%CrI),showpercentagesof

population,foreachagegrouporallagesoverall,estimatedtohavebeeninfectedbyMay16,

2020.IFR,median(95%CrI),wasestimatedhere,andaveragedoverMarch22-May16,2020;

weexcludedestimatesduringMarch1-21,2020,becauseestimateswerelessaccuratefor

theseearliestweekswhenzeroorfewdeathswerereported.

Age

Confirmed

Cases

Confirmedand

ProbableDeaths

Estimatedcumulative

infectionrate(%) EstimatedIFR(%)

<25 14692 40 8(5.1,16.7) 0.011(0.005,0.016)

25-44 60474 688 20.1(14.4,30) 0.12(0.077,0.15)

45-64 69839 4457 20.7(15.7,28) 0.94(0.74,1.21)

65-74 23875 4866 14.9(11.2,22.8) 4.67(3.22,6.66)

75+ 22512 10090 12.9(9.9,19.9) 13.83(9.65,17.78)

all 191392 20141 15.8(11.4,24.4) 1.45(1.09,1.87)



https://doi.org/10.1101/2020.06.27.20141689

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Figures Figure 1. Model fit. Black boxes show model estimates of cases per 100,000 population and grey boxes show model estimates of mortality rates; thick horizontal lines and box edges show the median, 25th, and 75th percentiles; vertical lines extending from each box show 95% Crl. Blue dots indicate observed incidence rates and red dots show observed mortality rates.

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(D) 65−74 years (E) 75+ years (F) All ages

(A) <25 years (B) 25−44 years (C) 45−64 years

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r 100

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ed/Probable Deaths per 100,000



https://doi.org/10.1101/2020.06.27.20141689

16

Figure 2. Estimated infection and case reporting rates over time. Boxplots show estimated infection rates. Red lines show the estimated median case reporting rate with surrounding areas show the 50% and 95% CrI. x-axis shows the first day of each week (mm/dd) from the week of March 1 to the week of March 10, 2020.

010

2030

4050

60R

epor

ting

Rat

e (%

)

03/01 03/22 04/12 05/03

010

0020

0030

0040

00In

fect

ions

per

100

,000

(A) <25 years

010

2030

4050

60R

epor

ting

Rat

e (%

)

03/01 03/22 04/12 05/03

020

0040

0060

0080

00In

fect

ions

per

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,000

(B) 25−44 years

010

2030

4050

60R

epor

ting

Rat

e (%

)

03/01 03/22 04/12 05/03

020

0040

0060

0080

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fect

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per

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,000

(C) 45−64 years

010

2030

4050

60R

epor

ting

Rat

e (%

)

03/01 03/22 04/12 05/03

010

0030

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00In

fect

ions

per

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,000

(D) 65−74 years

010

2030

4050

60R

epor

ting

Rat

e (%

)

03/01 03/22 04/12 05/03

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0050

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fect

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per

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(E) 75+ years

010

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4050

60R

epor

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Rat

e (%

)

03/01 03/22 04/12 05/03

010

0030

0050

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fect

ions

per

100

,000

(F) all ages



https://doi.org/10.1101/2020.06.27.20141689

17

Figure 3. Estimated infection fatality risk. Red lines show the estimated median IFR with surrounding areas indicating the 50% and 95% CrI. For comparison, the grey bars show the number of deaths reported for each week from the week of March 1 to May 10, 2020.

03/01 03/22 04/12 05/03

02

46

8N

o. D

eath

s

0.00

00.

005

0.01

00.

015

Infe

ctio

n Fa

talit

y R

isk

(%)

(A) <25 years

03/01 03/22 04/12 05/03

050

100

150

No.

Dea

ths

0.00

0.05

0.10

0.15

Infe

ctio

n Fa

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y R

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(%)

(B) 25−44 years

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020

040

060

080

010

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eath

s

0.0

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Infe

ctio

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y R

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(%)

(C) 45−64 years

03/01 03/22 04/12 05/03

020

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0014

00N

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eath

s

02

46

810

Infe

ctio

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talit

y R

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(%)

(D) 65−74 years

03/01 03/22 04/12 05/03

050

010

0015

0020

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eath

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1015

20In

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Fata

lity

Ris

k (%

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https://doi.org/10.1101/2020.06.27.20141689

1

SupplementaryMaterial

TableS1.Priorrangesformainmodelparametersandvariables.Thespatial,temporal,andageresolutionofeachparameteror

variable,estimatedinthemodel-inferencesystem,isspecifiedinthecolumn"Resolution".Noteposteriorparameterestimatescan

extendoutsidethespecifiedpriorranges.

Parameter/variable Symbol Resolution Priorrange Source/rationale

Initialexposed E(t=0) neighborhood-andage-

groupspecific,estimated

forthebeginningofthe

WeekofMarch1,2020

300–8000totalcitywide,

scaledbypopulationsizefor

eachagegroupand

neighborhood

Largeuncertainties,usedvery

widerange

Initialinfectious I(t=0) neighborhood-andage-

groupspecific,,

estimatedforthe

beginningoftheWeekof

March1,2020

150–4000totalcitywide,

scaledbypopulationsizefor

eachagegroupand

neighborhood

Assumedtobehalftheinitial

exposed

Initialsusceptible S(t=0) neighborhood-andage-


forthebeginningofthe

WeekofMarch1,2020

N–E–I Assumedallweresusceptible

exceptforthoseinitially

exposed/infectious



https://doi.org/10.1101/2020.06.27.20141689

2

Populationsizein

eachagegroupand

neighborhood

N neighborhood-andage-

groupspecific

N/A NYCintercensalpopulation

estimatesfor20181

Citywide

transmissionrate

βcity Citywide,age-group

specific,estimatedfor

eachweek

[0.5,1]perdayoverall;scaled

bycontactrateforeachage

groupbasedoncontactdata

fromthePOLYMODstudy2

BasedonR0estimatesofaround

1.5-4forSARS-CoV-23-5

Scalingof

neighborhood

transmissionrate

bi neighborhood-andage-


foreachweek

[0.8,1.2]foragegroupsunder

65years;[0.5,1.5]forage

groups65orolder

Around1;largervariationfor

elderlygroupsbasedondata

Latencyperiod Z Citywide,age-group


eachweek

[2,5]days Incubationperiod:5.2days(95%

CI:4.1,7)3;latencyperiodislikely

shorterthantheincubationperiod

Infectiousperiod D Citywide,age-group


eachweek

[2,5]days Timefromsymptomonsetto

hospitalization:3.8days(95%CI:

0,12.0)inChina,6plus1-2days

viralsheddingbeforesymptom



https://doi.org/10.1101/2020.06.27.20141689

3

onset.Wedidnotdistinguish

symptomatic/asymptomatic

infections.

Multiplicative

factorformobility

m1 Citywide,age-group


eachweek

[1,2]for<1year;[0.5,1.5]for

threeagegroups1-24years;

[0.1,1.5]foragegroup25-44;

[1,2.5]foragegroups45or

older

Initialmodeltestingshowed

transmissionratesforyoungerage

groupsweremoresensitiveto

changesinmobilitywhereasthe

twooldestagegroupswerenot

sensitivetomobility.Forage

groupswithcontactrateslower

thantheaverage(basedonthe

POLYMODstudy2),weraisedthe

diagonalelementsinthemobility

matrixtothepoweroftherelative

contactrate(<1)toaccountfor

insensitivityoftransmissionratein

theseagegroupstomobility.



https://doi.org/10.1101/2020.06.27.20141689

4

Multiplicative

factorfor

neighborhood

connectivity

m2 Citywide,age-group


eachweek

[0.5,2] Likelyaround1butwithlarge

uncertainties

Meanoftimefrom

viralsheddingto

diagnosis

Tm Citywide,age-group


eachweek

[3,8]days Fromafewdaystoaweekfrom

symptomonsettodiagnosis/

reporting,6plus1-2daysofviral

shedding(beinginfectious)before

symptomonset

Standarddeviation

(SD)oftimefrom

viralsheddingto

diagnosis

Tsd Citywide,age-group


eachweek

[1,3]days Toallowvariationintimeto

diagnosis/reporting

Reportingrate r Citywide,age-group


eachweek

Startingfrom[0.001,0.05]at

time0andallowedtoincrease

overtimeusingspacere-

probing7

Largeuncertainties

Infectionfatality

risk(IFR)

Citywide,age-group


eachweek

[5,15]×10-4foragesunder25;

[5,15]×10-3forages25-44;[5,

15]×10-2forages45-64;[0.01,

Basedonpreviousestimates8but

extendtohavewiderranges



https://doi.org/10.1101/2020.06.27.20141689

5

0.1]forages65-74;[0.02,0.2]

forages75+;

Timefrom

diagnosistodeath

Citywide Gammadistributionwithmean

of9.36daysandSDof9.76

days

Basedonn=15,686COVID-19

confirmeddeathsinNYCasofMay

17,2020.

References:

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ZhaoJ,LiuM,TuW,ChenC,JinL,YangR,WangQ,ZhouS,WangR,LiuH,LuoY,LiuY,ShaoG,LiH,TaoZ,YangY,DengZ,LiuB,

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6. ZhangJ,LitvinovaM,WangW,WangY,DengX,ChenX,LiM,ZhengW,YiL,ChenX,WuQ,LiangY,WangX,YangJ,SunK,

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26Mar2014.

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GriffinJT,BaguelinM,BhatiaS,BoonyasiriA,CoriA,CucunubaZ,FitzJohnR,GaythorpeK,GreenW,HamletA,HinsleyW,

LaydonD,Nedjati-GilaniG,RileyS,vanElslandS,VolzE,WangH,WangY,XiX,DonnellyCA,GhaniAC,FergusonNM.Estimates

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