DDI.COVID-19.Survey Africa Health Research Institute <_value> NADA AHRI COVID-19 Surveillance in rural South Africa: April 2020 – December 2020 AHRI.COVID-19.Surveillance Kobus Herbst Mark Siedner Guy Harling

Thobeka Mngomezulu

Nomathamsanqa Majozi

Siyabonga Nxumalo

Njabulo Dayi

Resign Gunda

Anne Derache

Theresa Smit

Dickman Gareta

Greg Ording

Jaco Dreyer

Eugene Ehlers

 Africa Health Research Institute NADA Wellcome Trust SAPRIN 097410/Z/11/Z DSI-SAMRC v1.0.0 Covid-19, Surveillance, South Africa, Screening, Health and Demographic Surveillance System Covid-19, Surveillance, South Africa, Screening, Health and Demographic Surveillance System South Africa uMkhanyakude district in northern KwaZulu-Natal Household-and individual- level surveillance (COVID-19 symptomatic screening and epidemiologic risk), mental health, health behaviours, economic impacts of COVID-19 epidemic and non-pharmaceutical interventions, clinical data from COVID-19 testing site for suspects referred for testing ClinicalScreenData 554 152 HDSSHouseholdData 19375 13 HDSSIndividualData 173817 19 HouseholdInterviews 42386 58 IndividualData 125703 68 SuspectScreening 71529 57 554 554 121 250319 118121.89 77478.068 554 535 535 535 535 535 535 534 532 532 91 534 19 19 1 19 19 90 90 91 527 528 529 535 535 554 553 548 553 553 553 553 552 553 553 553 553 553 42 520 519 553 519 553 554 554 554 554 554 72 3 1 553 14 42 520 1 554 554 554 554 554 554 554 554 554 553 553 553 553 553 553 553 553 553 553 124 8 124 124 553 334 553 553 554 554 554 554 17 17 17 17 17 534 534 534 534 534 534 1 1 1 1 1 1 534 534 533 534 534 534 1 1 1 534 509 513 509 509 1 509 554 554 554 1 2 554 Unique Household identifier 19374 1 11 43678 24587.922 14316.409 Date on which HSE was collected 18505 2011-02-12 2021-02-09 Socio-economic index 18505 870 0.825 5.085 3.409 0.541 11 .. Source of drinking water 18494 881 1 Unpurified natural 2 Well 3 Tanker 4 Public tap 5 Piped yard tap 6 Borehole 7 Piped house Sysmiss Type of toilet 17843 1532 1 Bucket 2 Chemical toilet 3 Other pit latrine 4 Ventilated pit latrine 5 Flush toilet Sysmiss # Bedrooms 18505 870 92 4.844 10.35 Adults Missed Meals 18433 942 -1 Unknown/Missing No 1 Yes Sysmiss ChildrenMissedMeals 13543 5832 -1 Unknown/Missing No 1 Yes Sysmiss Perceived Financial Status 18461 914 1 Extremely poor 2 Poor 3 Getting by 4 Comfortable 5 Very comfortable Sysmiss 19234 141 Default 1 Rural 2 Peri-urban 3 Urban Sysmiss 19234 141 1 _default 2 _don't know 3 _missing 4 _non applicable 5 _other 6 _query 7 Banzaneni 8 Deprecated 9 Dukuduku 10 Dukumbane 11 Ebaswazini 12 Egula (Hlabisa) 13 Egula (Mdletshe) 14 Ekuphisweni 15 Empembeni 16 Esiyembeni 17 Gunjaneni 18 Hlabisa Mission 19 Hlambanyathi 20 Inhlawathi 21 Khalokazi 22 Kwahoho 23 KwaMsane (Isigodi) 24 KwaMsane (Township) 25 KwaMseme 26 Mabhokweni 27 Mabudeni 28 Macambini 29 Macekeni 30 Machibini 31 Madondo 32 Madwaleni 33 Mahunjini 34 Makhambane 35 Makhowe 36 Makopini 37 Mapheleni 38 Mathunzi 39 Matshamhlophe 40 Matshamnyama-East 41 Matshamnyama-West 42 Mfekayi 43 Mgangatho 44 Mshaya 45 Mthekwini 46 Mthwadlana 47 Mtubatuba 48 Mvutshini 49 Myeki 50 Ncwabakazi 51 Ndlovu Village 52 Ngondini 53 Nkolokotho 54 Nkombose 55 Nkundusi 56 Nomathiya 57 Nompondo 58 Nqopheni 59 Nsolweni 60 Ogengele 61 Ophaphasi (Mdletshe) 62 Ophaphasi (Mpukunyoni) 63 Ophondweni 64 Qakwini 65 Qunwane 66 Shikishela 67 Sovane 68 St Lucia 69 Stezi Sysmiss 19233 Municipal ward number 19233 142 Unique individual identfier 173817 11 249208 132138.502 73962.335 173817 1890-01-01 2019-12-31 173817 Unique Household identifier 173817 11 43486 18443.739 14116.918 Unique homestead/dwelling identifier 173817 11 92657 15282.647 17248.811 Is resident 173817 -1 Unknown/Missing No 1 Yes Date of last known status 173817 2000-01-02 2019-12-31 last known status of indivdiual 173817 1 Current 2 Died 3 Migrated 4 Refused 5 Lost to follow-up 9 Membership end Currently in education 144555 29262 No 1 Full time 2 Part time Sysmiss Highest education 144738 29079 -1 DKN None/LT 1 yr 1 G01 2 G02 3 G03 4 G04 5 G05 6 G06 7 G07 8 G08 9 G09 10 G10 11 G11 12 G12 21 Certificate 22 Diploma 23 Degree 24 Honours 25 Masters 26 Doctoral 31 ABET 1 32 ABET 2 33 ABET 3 34 ABET 4 Sysmiss Date of last known education 150306 2000-04-07 2021-03-08 Employed 103367 70450 No 1 Yes 2 Part-time Sysmiss Employment sector 22580 151237 1 Agriculture 2 Mining 3 Manufactoring 4 Utilities 5 Construction 7 Restaurant/Hotels/Sport 8 Transport/Communication 9 Finance 10 Education 11 Healthcare 12 Legal 13 Research 14 Domestic work 15 Military/Police 16 Informal sector 99 Other Sysmiss Is self employed 28875 144942 1 Yes 2 No Sysmiss Date of last known employment 110277 2000-04-07 2021-03-08 Receives state pension 151302 22515 -1 Unknown/Missing No 1 Yes Sysmiss Date of last known pensioner state 7639 1798-01-01 2021-03-02 Receives other state social support 151302 22515 -1 Unknown/Missing No 1 Yes Sysmiss Date of last known other grant state 28350 1798-01-01 2021-02-23 Interview key (identifier in XX-XX-XX-XX format) 42031 42031 355 56854902 56953815 56902100.595 28245.946 19937 22449 -999999999 45 -474444487.291 499359024.226 Surveillance component 42031 355 1 High intensity sample 2 Routine household surveillance 3 Call Centre household surveillance Sysmiss Data collection wave 42031 355 42031 355 1 99 50.747 39.242 42031 355 11 92957 18383.989 21347.607 Interview date 42031 2020-04-15 2020-12-10 Contact type 42031 355 1 Succesful 2 Refused call 3 Phone out of service 4 Phone not answered Sysmiss Contacted 42031 355 1 Yes 2 No 3 Don't know Sysmiss HH IntID 42022 364 11 43678 22269.876 14301.992 Consented 26855 15531 -999999999 1 Yes 2 No 3 Don't know Sysmiss Consent to weekly calls 7169 35217 -999999999 1 Yes 2 No 3 Don't know Sysmiss 3398 38988 -999999999 2 -5297231.872 72599752.866 Heard of COVID-19 25315 17071 1 Yes 2 No 3 Don't know Sysmiss Made Changes 25121 17265 1 Yes 2 No 3 Don't know Sysmiss Washed hands more often 24420 17966 No 1 Yes Sysmiss Avoiding crowded areas 24420 17966 No 1 Yes Sysmiss Avoided social events 24420 17966 No 1 Yes Sysmiss Avoided taking taxis 24420 17966 No 1 Yes Sysmiss Avoided going out 24420 17966 No 1 Yes Sysmiss Avoided going to work 24420 17966 No 1 Yes Sysmiss Avoided travelling long distances 24420 17966 No 1 Yes Sysmiss Using face masks 24420 17966 No 1 Yes Sysmiss Wearing gloves 24420 17966 No 1 Yes Sysmiss Using hand sanitizer 24420 17966 No 1 Yes Sysmiss Other 24420 17966 No 1 Yes Sysmiss Specify Other Changes 2243 How much do you feel you know about the COVID-19 pandemic? 25315 17071 Anyone visit home 25315 17071 1 Yes 2 No 3 Don't know Sysmiss Number of visitors 1349 41037 -3 60 2.054 2.713 Able to access medication 25315 17071 -999999999 1 Yes 2 No 3 Don't know Sysmiss Unable to access healthcare 25314 17072 -999999999 1 Yes 2 No 3 Don't know Sysmiss Access food and other household necessities 25314 17072 -999999999 1 Yes 2 No 3 Don't know Sysmiss Affected ability to earn money 25314 17072 -999999999 1 Yes 2 No 3 Don't know Sysmiss Lost a job 2703 39683 No 1 Yes Sysmiss On unpaid leave 2703 39683 No 1 Yes Sysmiss Other 2703 39683 No 1 Yes Sysmiss 25 Not pay bills 2703 39683 No 1 Yes Sysmiss Take out a loan 2703 39683 No 1 Yes Sysmiss Skip meals 2703 39683 No 1 Yes Sysmiss Other 2703 39683 No 1 Yes Sysmiss 117 Access to soap and water 25314 17072 -999999999 1 Always 2 Sometimes 3 Never Sysmiss Little interest or pleasure in doing things 25314 17072 -999999999 1 Not at all 2 Several days 3 More than half the days 4 Nearly every day Sysmiss Feeling down, depressed or hopeless 25314 17072 -999999999 1 Not at all 2 Several days 3 More than half the days 4 Nearly every day Sysmiss Feeling nervous, anxious or on edge 25314 17072 -999999999 1 Not at all 2 Several days 3 More than half the days 4 Nearly every day Sysmiss Not be able to stop or control worrying 25314 17072 -999999999 1 Not at all 2 Several days 3 More than half the days 4 Nearly every day Sysmiss Visit clinic 708 41678 -999999999 1 Yes 2 No 3 Don't know Sysmiss 221 42165 25313 17073 -2000000000 6 -158020.519 17777251.034 25313 17073 -2000000000 6 -158020.501 17777251.034 27321 15065 33 251978 113922.629 76378.237 27321 15065 -1 Unknown/Missing 1 Male 2 Female Sysmiss 27321 1914-05-04 2019-06-25 27321 15065 1 106 47.477 16.308 42031 355 -1 43354 695.56 4040.923 125703 125703 2020-04-15 2020-12-10 Surveillance component 125703 1 High intensity sample 2 Routine household surveillance 3 Call Centre household surveillance Data collection wave 125703 HH IntID 125676 27 11 43678 20351.94 14105.386 125703 23 252839 145546.482 73490.128 125703 -1 Unknown/Missing 1 Male 2 Female 125703 1798-01-01 2020-11-19 125703 222 26.937 20.941 125703 1 Yes 2 No 3 Don't know 125703 1 Yes 2 No 3 Don't know Date Diagnosed 3582 1798-01-01 2920-08-02 Prior Covid Test Result 3582 122121 1 Positive 2 Negative 3 Don't know Sysmiss Fever 111844 13859 -999999999 1 Yes 2 No 3 Don't know 4 Sysmiss Cough 111844 13859 -999999999 1 Yes 2 No 3 Don't know 4 Sysmiss Chills 111844 13859 -999999999 1 Yes 2 No 3 Don't know 4 Sysmiss Sore throat 111844 13859 -999999999 1 Yes 2 No 3 Don't know 4 Sysmiss Shortness of breath 111844 13859 -999999999 1 Yes 2 No 3 Don't know 4 Sysmiss Nausea / Vomiting 111844 13859 -999999999 1 Yes 2 No 3 Don't know 4 Sysmiss Diarrhea 111844 13859 -999999999 1 Yes 2 No 3 Don't know 4 Sysmiss Myalgia 111844 13859 -999999999 1 Yes 2 No 3 Don't know 4 Sysmiss General weakness 111844 13859 -999999999 1 Yes 2 No 3 Don't know 4 Sysmiss Irritability / Confusion 111844 13859 -999999999 1 Yes 2 No 3 Don't know 4 Sysmiss Loss of smell or taste 804 124899 1 Yes 2 No 3 Don't know Sysmiss Loss of taste 111040 14663 -999999999 1 Yes 2 No 3 Don't know 4 Sysmiss Loss of sense of smell 111040 14663 -999999999 1 Yes 2 No 3 Don't know 4 Sysmiss Other 111844 13859 -999999999 1 Yes 2 No 3 Don't know 4 Sysmiss Other symptoms 95 Lethargy 4857 120846 1 Yes 2 No 3 Don't know 4 Sysmiss Poor feeding 4857 120846 1 Yes 2 No 3 Don't know 4 Sysmiss Date of Symptoms 1069 2020-01-01 2020-12-10 Contact with a known COVID-19 case 111844 13859 -999999999 1 Yes 2 No 3 Don't know 4 Sysmiss Healthcare setting 324 125379 No 1 Yes Sysmiss Household setting 324 125379 No 1 Yes Sysmiss Work place 324 125379 No 1 Yes Sysmiss Public transport setting 324 125379 No 1 Yes Sysmiss Other 324 125379 No 1 Yes Sysmiss 49 Healthcare Worker 111844 13859 -999999999 1 Yes 2 No 3 Don't know 4 Sysmiss Healthcare Worker Role 114 125589 Nurse 1 Physician 2 Pharmacist 3 Counselor 4 Laboratory Worker 99 Other Sysmiss Other Healthcare Worker 63 Visited Healthcare Facility 111844 13859 -999999999 1 Yes 2 No 3 Don't know 4 Sysmiss Type of facility 664 125039 Travelled 111844 13859 -999999999 1 Yes 2 No 3 Don't know 4 Sysmiss Destination 61 125642 1 Foreign travel 2 South Africa 3 Both Sysmiss Eastern Cape 61 125642 No 1 Yes Sysmiss Free State 61 125642 No 1 Yes Sysmiss Gauteng 61 125642 No 1 Yes Sysmiss KwaZulu-Natal 61 125642 No 1 Yes Sysmiss Limpopo 61 125642 No 1 Yes Sysmiss Mpumalanga 61 125642 No 1 Yes Sysmiss Northern Cape 61 125642 No 1 Yes Sysmiss North West 61 125642 No 1 Yes Sysmiss Western Cape 61 125642 No 1 Yes Sysmiss International Travel 125703 Left Home 112135 13568 -999999999 1 Yes 2 No 3 Don't know Sysmiss Left Village 21327 104376 -999999999 1 Yes 2 No 3 Don't know Sysmiss Local Town 10454 115249 1 Yes 2 No 3 Don't know Sysmiss Beyond Subdistrict 10454 115249 1 Yes 2 No 3 Don't know Sysmiss To get food/medication 21327 104376 No 1 Yes Sysmiss To go to work 21327 104376 No 1 Yes Sysmiss To visit friends or family 21327 104376 No 1 Yes Sysmiss To get exercise 21327 104376 No 1 Yes Sysmiss To provide care 21327 104376 No 1 Yes Sysmiss Other 21327 104376 No 1 Yes Sysmiss Outcome 125703 -1 Incomplete assessment 1 CoVID suspect 2 CoVID contact 3 CoVID suspect - symptoms 4 Not CoVID suspect 5 CoVID contact : Non-CoVID symptoms & CoVID risk factors 6 Not CoVID suspect : Non-CoVID symptoms & NO CoVID risk factors 99 Previously diagnosed with CoVID Member answered questions rather than proxy 110778 14925 -999999999 No 1 Yes 2 Sysmiss Whether the member is able to visit the mobile clinic 194 125509 1 Yes 2 No 3 No, other Sysmiss 71529 23 252839 154756.669 73162.645 71515 14 -1 Unknown/Missing 1 Male 2 Female Sysmiss 71515 1798-01-01 2020-11-19 71515 14 222 26.892 20.834 Surveillance component 71515 14 1 High intensity sample 2 Routine household surveillance 3 Call Centre household surveillance Sysmiss Data collection wave 71515 14 71529 2020-04-15 2020-12-10 71515 14 1 Yes 2 No 3 Don't know Sysmiss Date Diagnosed 2038 1798-01-01 2920-08-02 Prior Covid Test Result 2038 69491 1 Positive 2 Negative 3 Don't know Sysmiss Fever 63447 8082 1 Yes 2 No 3 Don't know 4 Sysmiss Cough 63447 8082 1 Yes 2 No 3 Don't know 4 Sysmiss Chills 63447 8082 1 Yes 2 No 3 Don't know 4 Sysmiss Sore throat 63447 8082 1 Yes 2 No 3 Don't know 4 Sysmiss Shortness of breath 63447 8082 1 Yes 2 No 3 Don't know 4 Sysmiss Nausea / Vomiting 63447 8082 1 Yes 2 No 3 Don't know 4 Sysmiss Diarrhea 63447 8082 1 Yes 2 No 3 Don't know 4 Sysmiss Myalgia 63447 8082 1 Yes 2 No 3 Don't know 4 Sysmiss General weakness 63447 8082 1 Yes 2 No 3 Don't know 4 Sysmiss Irritability / Confusion 63447 8082 1 Yes 2 No 3 Don't know 4 Sysmiss Loss of smell or taste 20 71509 1 Yes 2 No 3 Don't know Sysmiss Loss of taste 63427 8102 1 Yes 2 No 3 Don't know 4 Sysmiss Loss of sense of smell 63427 8102 1 Yes 2 No 3 Don't know 4 Sysmiss Other 63447 8082 1 Yes 2 No 3 Don't know 4 Sysmiss Other symptoms 48 Lethargy 2862 68667 1 Yes 2 No 3 Don't know 4 Sysmiss Poor feeding 2862 68667 1 Yes 2 No 3 Don't know 4 Sysmiss Date of Symptoms 732 2020-01-01 2020-12-10 Outcome 71515 14 -1 Incomplete assessment 1 CoVID suspect 2 CoVID contact 3 CoVID suspect - symptoms 4 Not CoVID suspect 5 CoVID contact : Non-CoVID symptoms & CoVID risk factors 6 Not CoVID suspect : Non-CoVID symptoms & NO CoVID risk factors 99 Previously diagnosed with CoVID Sysmiss HH IntID 71515 14 11 43678 22542.629 14313.031 526 2020-04-15 2020-12-11 520 525 525 525 525 524 525 525 525 525 525 34 497 496 525 493 525 526 483 Covid-19 PCR 483 71046 526 526 526 526 71529 16 92957 19017.34 20346.884 Walk in to testing point 71529 No 1 Yes