key: cord-279828-es498qul authors: Boulle, Andrew; Davies, Mary-Ann; Hussey, Hannah; Ismail, Muzzammil; Morden, Erna; Vundle, Ziyanda; Zweigenthal, Virginia; Mahomed, Hassan; Paleker, Masudah; Pienaar, David; Tembo, Yamanya; Lawrence, Charlene; Isaacs, Washiefa; Mathema, Hlengani; Allen, Derick; Allie, Taryn; Bam, Jamy-Lee; Buddiga, Kasturi; Dane, Pierre; Heekes, Alexa; Matlapeng, Boitumelo; Mutemaringa, Themba; Muzarabani, Luckmore; Phelanyane, Florence; Pienaar, Rory; Rode, Catherine; Smith, Mariette; Tiffin, Nicki; Zinyakatira, Nesbert; Cragg, Carol; Marais, Frederick; Mudaly, Vanessa; Voget, Jacqueline; Davids, Jody; Roodt, Francois; van Zyl Smit, Nellis; Vermeulen, Alda; Adams, Kevin; Audley, Gordon; Bateman, Kathleen; Beckwith, Peter; Bernon, Marc; Blom, Dirk; Boloko, Linda; Botha, Jean; Boutall, Adam; Burmeister, Sean; Cairncross, Lydia; Calligaro, Gregory; Coccia, Cecilia; Corin, Chadwin; Daroowala, Remy; Dave, Joel A; De Bruyn, Elsa; De Villiers, Martin; Deetlefs, Mimi; Dlamini, Sipho; Du Toit, Thomas; Endres, Wilhelm; Europa, Tarin; Fieggan, Graham; Figaji, Anthony; Frankenfeld, Petro; Gatley, Elizabeth; Gina, Phindile; Govender, Evashan; Grobler, Rochelle; Gule, Manqoba Vusumuzi; Hanekom, Christoff; Held, Michael; Heynes, Alana; Hlatswayo, Sabelo; Hodkinson, Bridget; Holtzhausen, Jeanette; Hoosain, Shakeel; Jacobs, Ashely; Kahn, Miriam; Kahn, Thania; Khamajeet, Arvin; Khan, Joubin; Khan, Riaasat; Khwitshana, Alicia; Knight, Lauren; Kooverjee, Sharita; Krogscheepers, Rene; Jacque Kruger, Jean; Kuhn, Suzanne; Laubscher, Kim; Lazarus, John; Le Roux, Jacque; Lee Jones, Scott; Levin, Dion; Maartens, Gary; Majola, Thina; Manganyi, Rodgers; Marais, David; Marais, Suzaan; Maritz, Francois; Maughan, Deborah; Mazondwa, Simthandile; Mbanga, Luyanda; Mbatani, Nomonde; Mbena, Bulewa; Meintjes, Graeme; Mendelson, Marc; Möller, Ernst; Moore, Allison; Ndebele, Babalwa; Nortje, Marc; Ntusi, Ntobeko; Nyengane, Funeka; Ofoegbu, Chima; Papavarnavas, Nectarios; Peter, Jonny; Pickard, Henri; Pluke, Kent; Raubenheimer, Peter J; Robertson, Gordon; Rozmiarek, Julius; Sayed, A; Scriba, Matthias; Sekhukhune, Hennie; Singh, Prasun; Smith, Elsabe; Soldati, Vuyolwethu; Stek, Cari; van den berg, Robert; van der Merwe, Le Roux; Venter, Pieter; Vermooten, Barbra; Viljoen, Gerrit; Viranna, Santhuri; Vogel, Jonno; Vundla, Nokubonga; Wasserman, Sean; Zitha, Eddy; Lomas-Marais, Vanessa; Lombard, Annie; Stuve, Katrin; Viljoen, Werner; Basson, De Vries; Le Roux, Sue; Linden-Mars, Ethel; Victor, Lizanne; Wates, Mark; Zwanepoel, Elbe; Ebrahim, Nabilah; Lahri, Sa'ad; Mnguni, Ayanda; Crede, Thomas; de Man, Martin; Evans, Katya; Hendrikse, Clint; Naude, Jonathan; Parak, Moosa; Szymanski, Patrick; Van Koningsbruggen, Candice; Abrahams, Riezaah; Allwood, Brian; Botha, Christoffel; Henndrik Botha, Matthys; Broadhurst, Alistair; Claasen, Dirkie; Daniel, Che; Dawood, Riyaadh; du Preez, Marie; Du Toit, Nicolene; Erasmus, Kobie; Koegelenberg, Coenraad F N; Gabriel, Shiraaz; Hugo, Susan; Jardine, Thabiet; Johannes, Clint; Karamchand, Sumanth; Lalla, Usha; Langenegger, Eduard; Louw, Eize; Mashigo, Boitumelo; Mhlana, Nonte; Mnqwazi, Chizama; Moodley, Ashley; Moodley, Desiree; Moolla, Saadiq; Mowlana, Abdurasiet; Nortje, Andre; Olivier, Elzanne; Parker, Arifa; Paulsen, Chané; Prozesky, Hans; Rood, Jacques; Sabela, Tholakele; Schrueder, Neshaad; Sithole, Nokwanda; Sithole, Sthembiso; Taljaard, Jantjie J; Titus, Gideon; Van Der Merwe, Tian; van Schalkwyk, Marije; Vazi, Luthando; Viljoen, Abraham J; Yazied Chothia, Mogamat; Naidoo, Vanessa; Alan Wallis, Lee; Abbass, Mumtaz; Arendse, Juanita; Armien, Rizqa; Bailey, Rochelle; Bello, Muideen; Carelse, Rachel; Forgus, Sheron; Kalawe, Nosi; Kariem, Saadiq; Kotze, Mariska; Lucas, Jonathan; McClaughlin, Juanita; Murie, Kathleen; Najjaar, Leilah; Petersen, Liesel; Porter, James; Shaw, Melanie; Stapar, Dusica; Williams, Michelle; Aldum, Linda; Berkowitz, Natacha; Girran, Raakhee; Lee, Kevin; Naidoo, Lenny; Neumuller, Caroline; Anderson, Kim; Begg, Kerrin; Boerlage, Lisa; Cornell, Morna; de Waal, Renée; Dudley, Lilian; English, René; Euvrard, Jonathan; Groenewald, Pam; Jacob, Nisha; Jaspan, Heather; Kalk, Emma; Levitt, Naomi; Malaba, Thoko; Nyakato, Patience; Patten, Gabriela; Schneider, Helen; Shung King, Maylene; Tsondai, Priscilla; Van Duuren, James; van Schaik, Nienke; Blumberg, Lucille; Cohen, Cheryl; Govender, Nelesh; Jassat, Waasila; Kufa, Tendesayi; McCarthy, Kerrigan; Morris, Lynn; Hsiao, Nei-yuan; Marais, Ruan; Ambler, Jon; Ngwenya, Olina; Osei-Yeboah, Richard; Johnson, Leigh; Kassanjee, Reshma; Tamuhla, Tsaone title: Risk factors for COVID-19 death in a population cohort study from the Western Cape Province, South Africa date: 2020-08-29 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1198 sha: doc_id: 279828 cord_uid: es498qul BACKGROUND: Risk factors for COVID-19 death in sub-Saharan Africa and the effects of HIV and tuberculosis on COVID-19 outcomes are unknown. METHODS: We conducted a population cohort study using linked data from adults attending public sector health facilities in the Western Cape, South Africa. We used Cox-proportional hazards models adjusted for age, sex, location and comorbidities to examine the association between HIV, tuberculosis and COVID-19 death from 1 March-9 June 2020 among (i) public sector “active patients” (≥1 visit in the 3 years before March 2020), (ii) laboratory-diagnosed COVID-19 cases and (iii) hospitalized COVID-19 cases. We calculated the standardized mortality ratio (SMR) for COVID-19 comparing HIV positive vs. negative adults using modelled population estimates. RESULTS: Among 3,460,932 patients (16% HIV positive), 22,308 were diagnosed with COVID-19, of whom 625 died. COVID-19 death was associated with male sex, increasing age, diabetes, hypertension and chronic kidney disease. HIV was associated with COVID-19 mortality (adjusted hazard ratio [aHR] 2.14; 95% confidence interval [CI] 1.70-2.70), with similar risks across strata of viral load and immunosuppression. Current and previous tuberculosis were associated with COVID-19 death (aHR [95%CI] 2.70 [1.81-4.04] and 1.51 [1.18-1.93] respectively). The SMR for COVID-19 death associated with HIV was 2.39 (95%CI 1.96-2.86); population attributable fraction 8.5% (95%CI 6.1-11.1). CONCLUSION: While our findings may over-estimate HIV- and tuberculosis-associated COVID-19 mortality risks due to residual confounding, both HIV and current tuberculosis were independently associated with increased COVID-19 mortality. The associations between age, sex and other comorbidities and COVID-19 mortality were similar to other settings. The effects of the intersecting pandemics of HIV, tuberculosis and coronavirus disease-19 in sub-Saharan Africa are unknown. Studies to date suggest no increased risk of adverse outcomes in HIV co-infected patients, but these are small studies from Europe and North America, often limited to hospitalized patients, and may not be relevant to sub-Saharan Africa where people living with HIV (PLWH) are younger with different comorbidities, frequently including tuberculosis [1] [2] [3] [4] [5] [6] [7] [8] . PLWH may experience more severe COVID-19 disease due to HIV-related immune suppression, which may be exacerbated by transient immune deficiency from coronaviruses [9, 10] . In support of this hypothesis a large UK cohort study reported increased risk of COVID-19 death with immunosuppressive comorbidity, including PLWH [8] . Two factors may reduce risk of severe COVID-19 in PLWH, however: dysfunctional immunity may lessen a virus-induced cytokine storm [11, 12] , and some antiretroviral drugs (tenofovir and some protease inhibitors) have in vitro activity against coronaviruses, with better outcomes reported for PLWH receiving tenofovir disoproxil fumarate (TDF) vs. other antiretrovirals [12, 13] . Tuberculosis may exacerbate COVID-19 with impaired immune responses and increased angiotensin converting enzyme 2 receptor expression in respiratory epithelial cells, while COVID-19 pneumonia may enhance tuberculosis progression [14] [15] [16] [17] . It is important to establish if HIV and tuberculosis increase risk of COVID-19 death so that patients with these conditions can be provided with augmented prevention and potential therapeutic interventions. We used linked data from adults attending public sector health facilities in the Western Cape Province, South Africa, to identify factors associated with COVID-19 death. 9 We conducted a cohort study using de-identified data from the Western Cape Provincial Health Data Centre (WCPHDC) of public sector patients aged ≥20 years with documented sex and not known to have died before March 1, 2020 (before the first diagnosed COVID-19 case in South Africa, and several weeks before the first documented COVID-19 death) and included all follow up through June 9, 2020. The outcome was COVID-19 associated death. Our main analysis examined risk of COVID-19 death in the general population, so all patients were included irrespective of SARS-CoV-2 testing. The study was approved by the University of Cape Town and Stellenbosch University Health Research Ethics Committees and the Western Cape Province Department of Health. Individual informed consent requirement was waived for this secondary analysis of de-identified data. The Western Cape has nearly 7 million inhabitants, of whom ~520,000 are PLWH with >90% of them dependent on public sector health services. The WCPHDC has been described in detail [18] . Briefly, WCPHDC consolidates administrative, laboratory, and pharmacy data from routine electronic clinical information systems used in all public sector health facilities with linkage through a unique identifier. Multiple data sources are triangulated to enumerate health conditions such as diabetes mellitus ("diabetes"), hypertension, tuberculosis and HIV, with high or moderate certainty evidence assigned for each inferred condition (Supplementary Table 1 ). High certainty evidence of HIV comprises a positive HIV diagnostic test and/or HIV-RNA test and/or triple antiretroviral therapy (ART) and/or registration in the HIV disease management system; moderate certainty is assigned for those with only a CD4 count measure and/or two antiretroviral drugs prescribed (previously used for vertical HIV transmission prevention) and/or ICD-10 diagnosis code of HIV. HIV testing coverage is high, as >90% of PLWH know their HIV diagnosis [19] . High certainty evidence of tuberculosis comprised laboratory evidence of Mycobacterium tuberculosis infection (any anatomical site, using Xpert RIF/MTB, microscopy, culture) and/or registration on the electronic tuberculosis registers and/or combination tuberculosis treatment and/or admission to a tuberculosis hospital. Comorbidities were based on high or moderate certainty evidence but restricted to high certainty evidence in sensitivity analyses. The virologic, immunologic and ART status of PLWH on March 1, 2020 was categorized, based on most recent measures, as "confirmed virologically suppressed on ART" (HIV-RNA<1000 copies/ml in last 15 months and ART dispensed in last 6 months), "likely virologically suppressed on ART" (HIV-RNA <1000 copies/ml 15-24 months previously or HIV-RNA <1000 copies/ml >24 months previously if ART dispensed in last 6 months), "viraemic or immunosuppressed" (HIV-RNA >1000 copies/ml in last 15 months or CD4 count <200 cells/µl within 18 months before March 2020) or "unknown". Until January 2020, adult first-line ART was TDF+emtricitabine/lamivudine+efavirenz, with abacavir replacing TDF for patients with kidney disease; zidovudine+emtricitabine/lamivudine+protease inhibitor was used for second-line ART for most patients. Dolutegravir was introduced in first and second-line since January 2020. Diabetic control was categorized according to glycosylated haemoglobin (HbA1c) measurement within the last 2 years as <7% (controlled); 7-8.9% (poorly controlled), ≥9% (uncontrolled). All COVID-19 diagnoses were based on a positive SARS-CoV-2 PCR test. Testing was available for all patients with COVID-19 symptoms until June 1, 2020; thereafter public sector laboratory testing was restricted to patients requiring admission or aged >55 years or 11 with comorbidities, due to temporary limited testing capacity. Hospital admissions and all deaths in SARS-CoV-2 positive cases are recorded and reviewed daily. We used Cox-proportional hazards models adjusted for age, sex and other comorbidities to examine the association between HIV, tuberculosis and COVID-19 death among (i) all public sector patients with ≥1 health visit in the 3 years before March 1, 2020 (considered "active patients"), (ii) laboratory-diagnosed COVID-19 cases and (iii) hospitalized COVID-19 cases. We adjusted for location within Cape Town vs. rest of the province and subdistrict of residence within Cape Town to account for geographical variation in infection rates and as a proxy for socio-economic status. Patients were censored on date of death if deceased without a COVID-19 diagnosis, or on June 9, 2020, whichever was earliest. Database closure was 7 days later to allow for death reporting delays. For the analysis of COVID-19 death in laboratory-diagnosed cases we included cases diagnosed before June 1, 2020 when testing was available for all patients with COVID-19 symptoms, but included all patients diagnosed by June 9, 2020 in sensitivity analysis. The proportional-hazard assumption was assessed with Schoenfeld residuals [20] . All analyses were conducted using Stata 15.1. We also calculated the standardized mortality ratio (SMR) of the actual number of COVID-19 deaths in PLWH vs. the number that would be expected if PLWH had the same risk of COVID-19 death as HIV-negative people of the same age and sex. We used data on the age, sex and HIV status of all COVID-19 deaths (public and private sector) and the Thembisa Western Cape HIV model to estimate the Western Cape population size and HIV prevalence, by age and sex, in 2020. [21] We calculated 95% confidence intervals (CI) for the SMR using 12 Since individual socio-economic status and some comorbidities are not recorded in WCPHDC, we calculated E-values to determine the minimum strength of association that an unmeasured confounder (e.g. raised body mass index [BMI] or socio-economic status) would need to have with HIV/ tuberculosis and COVID-19 death to fully account for any association between HIV/tuberculosis and COVID-19 death [22] . We conducted quantitative bias analysis to assess the impact of potential confounding by obesity on an association between HIV and COVID-19 death. Among 3,460,932 "active patients" aged ≥20 years on March 1, 2020, 22,308 were diagnosed with COVID-19, of whom 625 (2.8%) died (Table 1) . Among COVID-19 cases, 69% were diagnosed and 67% of deaths occurred before the change in testing criteria (June 1). The proportion of men was lower among COVID-19 cases vs. non-cases (31% vs. 42%), likely due to initial cases being among essential workers in retail and manufacturing sectors employing predominantly women. The proportion of women peaked (76%) in week 5 of the epidemic, declining thereafter. Diabetes and hypertension were common in all patients, with higher prevalence among COVID-19 cases than non-cases ( and previous tuberculosis 14% vs. 8%). 13 Although the proportion of PLWH was similar among surviving and deceased COVID-19 cases, a greater proportion of COVID-19 deaths were in patients aged <50 years in those with vs. without HIV (39% vs 13%) ( Table 2) . A substantial proportion of COVID-19 deceased PLWH had diabetes (50%) and hypertension (42%), however these conditions were more common in deceased people without HIV (62% for each condition). Current and previous tuberculosis were more frequent in PLWH irrespective of COVID-19 with 14% and 37% of COVID-19 deceased cases with HIV having current and/or previous tuberculosis respectively. Among all public sector patients, the probability of COVID-19 death by 100 days since Figure 1) . To assess whether the association between HIV or tuberculosis and COVID-19 mortality could be due to residual unmeasured confounding e.g. by socio-economic status, or unrecorded comorbidities, we calculated the E-value for an unmeasured confounder. For Among all laboratory diagnosed COVID-19 cases, there were 135 deaths among an estimated ~520,000 PLWH in the province (260 deaths/million) and 786 deaths among 6.36 million people without HIV (124 deaths/million). The SMR for COVID-19 mortality in PLWH, relative to HIV-negative people was 2.39 (95% CI 1.96-2.86) and the attributable fraction of public and private sector COVID-19 deaths due to HIV was 8.5% (95% CI 6.1-11.1). Among nearly 3.5 million adults (16% PLWH) in South Africa we found an approximately two-fold association of COVID-19 death with HIV, irrespective of viraemia or immunosuppression prior to the COVID-19 episode, and a similar association between COVID-19 death and current tuberculosis. Among PLWH on ART, receiving TDF was associated with lower COVID-19 mortality compared to other antiretrovirals. While the HIVand tuberculosis-associated increased risk of COVID-19 death may be over-estimated if there is residual confounding due to socio-economic status or unrecorded comorbidities, our results, supported by sensitivity analyses, demonstrate that PLWH and persons with tuberculosis are at increased risk of severe COVID-19. Nonetheless, despite a high burden of advanced HIV in the province, the attributable fraction of all deaths ascribed to HIV was <10%. While most case series of HIV and SARS-CoV-2 co-infection have not shown poor outcomes in PLWH, [1-3, 5-7] some cohorts of hospitalized PLWH with COVID-have reported substantial morbidity and mortality including among patients with suppressed viral load on ART [23, 24] London have not shown differences in mortality risk [25] [26] [27] , however, the absence of increased mortality risk in hospitalized patients with comorbidities may be explained by selection bias; risk factors for COVID-19 death may be attenuated by restricting to the subset of hospitalized patients already at high mortality risk [28] . It is therefore expected that in our analysis the increased risk of death associated with all comorbidities was progressively attenuated when restricting to cases (people with sufficiently severe symptoms to be tested) and hospitalized patients. Similar to our findings, several studies have reported a high prevalence of comorbidities among PLWH with severe COVID-19 [3, 6, 7] . The high prevalence of comorbidities in deceased PLWH suggests that the effect of HIV may at least partly be due to an increased risk of comorbidities at younger ages [2, 7] , including those not recorded in WCPHDC such as cardiovascular disease. Persistent immune dysfunction may also be important in severe COVID-19 despite viral suppression; the hazard ratio point estimates for association with COVID-19 death were greater in immunosuppressed or viraemic PLWH, although the numbers of these patients with COVID-19 were small with wide CIs. Further, CD4 <200 cells/µl during admission was associated with COVID-19 death. While this may partly be due to the well-described lymphopenia in severe COVID-19 which is prognostic of poor outcomes, about half of patients with low CD4 during admission were either new HIV diagnoses or had previous immunosuppression, viraemia or no recent ART [10] . Among COVID-19 cases in PLWH on ART, receipt of TDF (vs. other therapies) was associated with reduced COVID-19 mortality. However, this association is likely to be over-estimated; in South Africa only patients on second-line ART or with poor renal function would not be on TDF, and both of these factors may themselves increase mortality. Nonetheless, the association remained when adjusting for kidney disease, viral suppression and ART duration, and concurs with results from a recently published cohort of PLWH on ART from Spain [13] . We found both current and previous tuberculosis to be associated with COVID-19 death, but since current tuberculosis itself causes death, in the absence of autopsy evidence it is difficult to disentangle the effects of COVID-19 vs tuberculosis disease on mortality per se [17] . In our study, the overall high prevalence of diabetes in people with and without HIV, high proportion with poor glycaemic control and very elevated risks for COVID-19 death for diabetics compared to those reported from other countries are concerning [8] . Diabetes is often diagnosed late and/or untreated or poorly controlled in resource-limited settings, and the resulting microvascular disease even in people with good current diabetic control may increase COVID-19 mortality [29] . To our knowledge this is the largest report on SARS-CoV-2 from Africa, the largest report on Table 1 : Characteristics of (i) Western Cape "active patients" aged ≥20 years in public sector (public sector health care visit in last 3 years before March 1, 2020) according to COVID-19 outcome (ii) COVID-19 cases in "active patients" and (iii) hospitalized COVID-19 cases in "active patients". Reference category is HIV negative; restricted to HIV-negative patients and 199 of 601 PLWH with CD4 measurement at time of COVID-19 diagnosis or admission; adjusted for all other variables listed in this table in a model that included the listed categories of CD4 count instead of the binary variable HIV positive vs negative; the effect o f the other variables on mortality was similar to those presented here. HR hazard ratio; CI confidence interval; HbA1c glycosylated haemoglobin; VL viral load; ART antiretroviral therapy; mo months; yr years; PLWH people living with HIV Figure 1 : Comparison of adjusted hazard ratios (HR) and 95% confidence intervals (CI) for associations with COVID-19 death from Cox-proportional hazards models among (i) all public sector patients ≥20 years with a public sector health visit in the previous 3 years (n=3,460,932) (ii) all adult COVID-19 cases diagnosed before June 1, 2020 (n=15,203) and (iii) all hospitalized COVID-19 cases (n=2, 978). COVID-19 in patients with HIV: clinical case series Clinical features and outcomes of HIV patients with coronavirus disease 2019 COVID-19 in people living with human immunodeficiency virus: a case series of 33 patients COVID-19 in patients with HIV A Case Series of Five People Living with HIV Hospitalized with COVID-19 in Clinical characteristics and outcomes in people living with HIV hospitalized for COVID-19 Description of COVID-19 in HIV-infected individuals: a single-centre, prospective cohort OpenSAFELY: factors associated with COVID-19 death in 17 million patients Dysregulation of immune response in patients with COVID-19 in Wuhan, China Lymphopenia predicts disease severity of COVID-19: a descriptive and predictive study Could HIV infection alter the clinical course of SARS-CoV-2 infection? When less is better Why Aren't People Living with HIV at Higher Risk for Developing Severe Coronavirus Disease 2019 (COVID-19)? Incidence and Severity of COVID-19 in HIV-Positive Persons Receiving Antiretroviral Therapy: A Cohort Study Tuberculosis and type 2 Diabetes Mellitus: an inflammatory danger signal in the time of COVID-19 Tuberculosis, COVID-19 and migrants: preliminary analysis of deaths occurring in 69 patients from two cohorts Active tuberculosis, sequelae and COVID-19 co-infection: first cohort of 49 cases Active or latent tuberculosis increases susceptibility to COVID-19 and disease severity Data Centre Profile: The Provincial Health Data Centre of the Western Cape Province, South Africa Available at: www.thembisa.org 22. VanderWeele TJ, Ding P. Sensitivity Analysis in Observational Research: Introducing the E-Value Hospitalized patients with COVID-19 and HIV: a case series Clinical features and outcome of HIV/SARS-CoV-2 co-infected patients in the Bronx Outcomes among HIV-positive patients hospitalized with COVID-19 Covid-19 and People with HIV Infection: Outcomes for Hospitalized Patients Comparative outcomes in hospital admissions with COVID-19 in people living with HIV and people living without HIV: A retrospective study Diabetes mellitus in Zambia and the Western Cape province of South Africa: Prevalence, risk factors, diagnosis and management Reference category for hazard ratio is HIV negative; only included in adjusted analysis; adjusted for all other variables listed in this table in a model that included the listed categories of HIV viral load (VL), antiretroviral therapy (ART) and immunosuppression instead of the binary variable HIV positive vs negative; the effect of the other variables on mortality was similar to those presented here. HR hazard ratio; CI confidence interval; HbA1c glycosylated haemoglobin; VL viral load; ART antiretroviral therapy All public-sector SARS-CoV-2 cases diagnosed before 1 June2020