Communicable and non-communicable co-morbidities and the presentation of COVID-19 in an African setting of high HIV-1 and tuberculosis prevalence. Du Bruyn, E., Stek, C., Daroowala, R., Said-Hartley, Q., Hsiao, M., Goliath, R. T., Abrahams, F., Jackson, A., Wasserman, S., Allwood, B. W, Davis, A. G, Lai, R. P., Coussens, A. K, Wilkinson, K. A, de Vries, J., Tiffin, N., Cerrone, M., Ntusi, N. A B, Riou, C., Wilkinson, R. J, Investigators, o. b. o. t. H., Aziz, S., Bangani, N., Black, J., Bremer, M., Burgers, W., Ciko, Z., Esmail, H., Gordon, S., Harley, Y. X R, Lakay, F., Martinez-Estrada, F., Meintjes, G. A, Mendelson, M., Papavarnavas, T., Proust, A., Ruzive, S., Schafer, G., Serole, K., Whitaker, C., & Zvinairo, K. medRxiv, Cold Spring Harbor Laboratory Press, may, 2021. Paper doi abstract bibtex 1 download Objectives To describe the presentation and outcome of SARS-CoV2 infection in an African setting of high non-communicable co-morbidity and also HIV-1 and tuberculosis prevalence. Design Case control analysis with cases stratified by HIV-1 and tuberculosis status. Setting A single-centre observational case-control study of adults admitted to a South African hospital with proven SARS-CoV-2 infection or alternative diagnosis. Participants 104 adults with RT-PCR-proven SARS-CoV2 infection of which 55 (52.9%) were male and 31 (29.8%) HIV-1 co-infected. 40 adults (35.7% male, 30.9% HIV-1 co-infected) admitted during the same period with no RT-PCR or serological evidence of SARS-CoV2 infection and assigned alternative diagnoses. Additional in vitro data from prior studies of 72 healthy controls and 118 HIV-1 uninfected and infected persons participants enrolled to a prior study with either immune evidence of tuberculosis sensitization but no symptoms or microbiologically confirmed pulmonary tuberculosis. Results Two or more co-morbidities were present in 57.7% of 104 RT-PCR proven COVID-19 presentations, the commonest being hypertension (48%), type 2 diabetes mellitus (39%), obesity (31%) but also HIV-1 (30%) and active tuberculosis (14%). Amongst patients dually infected by tuberculosis and SARS-CoV-2, clinical features could be dominated by either SARS-CoV-2 or tuberculosis: lymphopenia was exacerbated, and some markers of inflammation (D-dimer and ferritin) elevated in singly SARS-CoV-2 infected patients were even further elevated (p \textless 0.05). HIV-1 and SARS-CoV2 co-infection resulted in lower absolute number and proportion of CD4 lymphocytes, with those in the lowest peripheral CD4 percentage strata exhibiting absent or lower antibody responses against SARS-CoV2. Death occurred in 30/104 (29%) of all COVID-19 patients and in 6/15 (40%) of patients with coincident SARS-CoV-2 and tuberculosis. Conclusions In this South African setting, HIV-1 and tuberculosis are common co-morbidities in patients presenting with COVID-19. In environments in which tuberculosis is common, SARS-CoV-2 and tuberculosis may co-exist with clinical presentation being typical of either disease. Clinical suspicion of exacerbation of co-existent tuberculosis accompanying SARS-CoV-2 should be high. What is already known on this topic? It has been quite widely thought that Africa has been spared the worst effects of the COVID-19 pandemic. There are very few reported case series and no case-control studies comparing COVID-19 patients admitted to hospital to those admitted for other reasons. However several studies have indicated both HIV-1 and tuberculosis co-infection that are endemic in Africa constitute risk factors for poor outcome. In addition Africa is subject to demographic transition and the prevalence of non-communicable co-morbidities such as type 2 diabetes, hypertension and cardiovascular disease is rising rapidly. No study from Africa has described the clinical impact on the presentation of COVID-19 infection. What this study adds Two or more co-morbidities were present in over half COVID-19 presentations, including HIV-1 (30%) and active tuberculosis (14%). Patients dually infected by tuberculosis and SARS-CoV-2, presented as either SARS-CoV-2 or tuberculosis. HIV-1 and SARS-CoV2 co-infection resulted in lower absolute number and proportion of CD4 lymphocytes, and those with low CD4 counts had absent or lower antibody responses against SARS-CoV2. Death occurred 29% of all COVID-19 patients and in 40% of patients with coincident SARS-CoV-2 and tuberculosis. Thus in environments in which tuberculosis is common, SARS-CoV-2 and tuberculosis may co-exist with clinical presentation being typical of either disease and clinical suspicion of exacerbation of co-existent tuberculosis accompanying SARS-CoV-2 should be high. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This research was funded in whole, or in part, by Wellcome [104803, 203135, 222754]. For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. RJW was supported by the Francis Crick Institute which receives its core funding from Cancer Research UK (FC0010218), the UK Medical Research Council (FC0010218), and Wellcome (FC0010218). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The study was approved by the University of Cape Town Health Sciences Research Ethical Committee (HREC 207/2020) All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes Data will be made available following formal publication via contact with the corresponding author
@article{Bruyn2021,
abstract = {Objectives To describe the presentation and outcome of SARS-CoV2 infection in an African setting of high non-communicable co-morbidity and also HIV-1 and tuberculosis prevalence. Design Case control analysis with cases stratified by HIV-1 and tuberculosis status. Setting A single-centre observational case-control study of adults admitted to a South African hospital with proven SARS-CoV-2 infection or alternative diagnosis. Participants 104 adults with RT-PCR-proven SARS-CoV2 infection of which 55 (52.9{\%}) were male and 31 (29.8{\%}) HIV-1 co-infected. 40 adults (35.7{\%} male, 30.9{\%} HIV-1 co-infected) admitted during the same period with no RT-PCR or serological evidence of SARS-CoV2 infection and assigned alternative diagnoses. Additional in vitro data from prior studies of 72 healthy controls and 118 HIV-1 uninfected and infected persons participants enrolled to a prior study with either immune evidence of tuberculosis sensitization but no symptoms or microbiologically confirmed pulmonary tuberculosis. Results Two or more co-morbidities were present in 57.7{\%} of 104 RT-PCR proven COVID-19 presentations, the commonest being hypertension (48{\%}), type 2 diabetes mellitus (39{\%}), obesity (31{\%}) but also HIV-1 (30{\%}) and active tuberculosis (14{\%}). Amongst patients dually infected by tuberculosis and SARS-CoV-2, clinical features could be dominated by either SARS-CoV-2 or tuberculosis: lymphopenia was exacerbated, and some markers of inflammation (D-dimer and ferritin) elevated in singly SARS-CoV-2 infected patients were even further elevated (p {\textless} 0.05). HIV-1 and SARS-CoV2 co-infection resulted in lower absolute number and proportion of CD4 lymphocytes, with those in the lowest peripheral CD4 percentage strata exhibiting absent or lower antibody responses against SARS-CoV2. Death occurred in 30/104 (29{\%}) of all COVID-19 patients and in 6/15 (40{\%}) of patients with coincident SARS-CoV-2 and tuberculosis. Conclusions In this South African setting, HIV-1 and tuberculosis are common co-morbidities in patients presenting with COVID-19. In environments in which tuberculosis is common, SARS-CoV-2 and tuberculosis may co-exist with clinical presentation being typical of either disease. Clinical suspicion of exacerbation of co-existent tuberculosis accompanying SARS-CoV-2 should be high. What is already known on this topic? It has been quite widely thought that Africa has been spared the worst effects of the COVID-19 pandemic. There are very few reported case series and no case-control studies comparing COVID-19 patients admitted to hospital to those admitted for other reasons. However several studies have indicated both HIV-1 and tuberculosis co-infection that are endemic in Africa constitute risk factors for poor outcome. In addition Africa is subject to demographic transition and the prevalence of non-communicable co-morbidities such as type 2 diabetes, hypertension and cardiovascular disease is rising rapidly. No study from Africa has described the clinical impact on the presentation of COVID-19 infection. What this study adds Two or more co-morbidities were present in over half COVID-19 presentations, including HIV-1 (30{\%}) and active tuberculosis (14{\%}). Patients dually infected by tuberculosis and SARS-CoV-2, presented as either SARS-CoV-2 or tuberculosis. HIV-1 and SARS-CoV2 co-infection resulted in lower absolute number and proportion of CD4 lymphocytes, and those with low CD4 counts had absent or lower antibody responses against SARS-CoV2. Death occurred 29{\%} of all COVID-19 patients and in 40{\%} of patients with coincident SARS-CoV-2 and tuberculosis. Thus in environments in which tuberculosis is common, SARS-CoV-2 and tuberculosis may co-exist with clinical presentation being typical of either disease and clinical suspicion of exacerbation of co-existent tuberculosis accompanying SARS-CoV-2 should be high. {\#}{\#}{\#} Competing Interest Statement The authors have declared no competing interest. {\#}{\#}{\#} Funding Statement This research was funded in whole, or in part, by Wellcome [104803, 203135, 222754]. For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. RJW was supported by the Francis Crick Institute which receives its core funding from Cancer Research UK (FC0010218), the UK Medical Research Council (FC0010218), and Wellcome (FC0010218). {\#}{\#}{\#} Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The study was approved by the University of Cape Town Health Sciences Research Ethical Committee (HREC 207/2020) All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes Data will be made available following formal publication via contact with the corresponding author},
author = {{Du Bruyn}, Elsa and Stek, Cari and Daroowala, Remi and Said-Hartley, Qonita and Hsiao, Marvin and Goliath, Rene T. and Abrahams, Fatima and Jackson, Amanda and Wasserman, Sean and Allwood, Brian W and Davis, Angharad G and Lai, Rachel P-J. and Coussens, Anna K and Wilkinson, Katalin A and de Vries, Jantina and Tiffin, Nicki and Cerrone, Maddalena and Ntusi, Ntobeko A B and Riou, Catherine and Wilkinson, Robert J and Investigators, on behalf of the HIATUS and Aziz, Saalikha and Bangani, Nonzwakazi and Black, John and Bremer, Marise and Burgers, Wendy and Ciko, Zandile and Esmail, Hanif and Gordon, Siamon and Harley, Yolande X R and Lakay, Francisco and Martinez-Estrada, Fernando-Oneissi and Meintjes, Graeme A and Mendelson, Marc and Papavarnavas, Tari and Proust, Alize and Ruzive, Sheena and Schafer, Georgia and Serole, Keboile and Whitaker, Claire and Zvinairo, Kennedy},
doi = {10.1101/2021.05.11.21256479},
file = {:C$\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Du Bruyn et al. - 2021 - Communicable and non-communicable co-morbidities and the presentation of COVID-19 in an African setting of high.pdf:pdf},
journal = {medRxiv},
keywords = {OA,OA{\_}PMC,fund{\_}ack,genomics{\_}fund{\_}ack,original},
mendeley-tags = {OA,OA{\_}PMC,fund{\_}ack,genomics{\_}fund{\_}ack,original},
month = {may},
pages = {2021.05.11.21256479},
publisher = {Cold Spring Harbor Laboratory Press},
title = {{Communicable and non-communicable co-morbidities and the presentation of COVID-19 in an African setting of high HIV-1 and tuberculosis prevalence}},
url = {https://www.medrxiv.org/content/10.1101/2021.05.11.21256479v1 https://www.medrxiv.org/content/10.1101/2021.05.11.21256479v1.abstract},
year = {2021}
}
Downloads: 1
{"_id":"i9kcru2cXPPPfWxzG","bibbaseid":"dubruyn-stek-daroowala-saidhartley-hsiao-goliath-abrahams-jackson-etal-communicableandnoncommunicablecomorbiditiesandthepresentationofcovid19inanafricansettingofhighhiv1andtuberculosisprevalence-2021","author_short":["Du Bruyn, E.","Stek, C.","Daroowala, R.","Said-Hartley, Q.","Hsiao, M.","Goliath, R. T.","Abrahams, F.","Jackson, A.","Wasserman, S.","Allwood, B. W","Davis, A. G","Lai, R. P.","Coussens, A. K","Wilkinson, K. A","de Vries, J.","Tiffin, N.","Cerrone, M.","Ntusi, N. A B","Riou, C.","Wilkinson, R. J","Investigators, o. b. o. t. H.","Aziz, S.","Bangani, N.","Black, J.","Bremer, M.","Burgers, W.","Ciko, Z.","Esmail, H.","Gordon, S.","Harley, Y. X R","Lakay, F.","Martinez-Estrada, F.","Meintjes, G. A","Mendelson, M.","Papavarnavas, T.","Proust, A.","Ruzive, S.","Schafer, G.","Serole, K.","Whitaker, C.","Zvinairo, K."],"bibdata":{"bibtype":"article","type":"article","abstract":"Objectives To describe the presentation and outcome of SARS-CoV2 infection in an African setting of high non-communicable co-morbidity and also HIV-1 and tuberculosis prevalence. Design Case control analysis with cases stratified by HIV-1 and tuberculosis status. Setting A single-centre observational case-control study of adults admitted to a South African hospital with proven SARS-CoV-2 infection or alternative diagnosis. Participants 104 adults with RT-PCR-proven SARS-CoV2 infection of which 55 (52.9%) were male and 31 (29.8%) HIV-1 co-infected. 40 adults (35.7% male, 30.9% HIV-1 co-infected) admitted during the same period with no RT-PCR or serological evidence of SARS-CoV2 infection and assigned alternative diagnoses. Additional in vitro data from prior studies of 72 healthy controls and 118 HIV-1 uninfected and infected persons participants enrolled to a prior study with either immune evidence of tuberculosis sensitization but no symptoms or microbiologically confirmed pulmonary tuberculosis. Results Two or more co-morbidities were present in 57.7% of 104 RT-PCR proven COVID-19 presentations, the commonest being hypertension (48%), type 2 diabetes mellitus (39%), obesity (31%) but also HIV-1 (30%) and active tuberculosis (14%). Amongst patients dually infected by tuberculosis and SARS-CoV-2, clinical features could be dominated by either SARS-CoV-2 or tuberculosis: lymphopenia was exacerbated, and some markers of inflammation (D-dimer and ferritin) elevated in singly SARS-CoV-2 infected patients were even further elevated (p \\textless 0.05). HIV-1 and SARS-CoV2 co-infection resulted in lower absolute number and proportion of CD4 lymphocytes, with those in the lowest peripheral CD4 percentage strata exhibiting absent or lower antibody responses against SARS-CoV2. Death occurred in 30/104 (29%) of all COVID-19 patients and in 6/15 (40%) of patients with coincident SARS-CoV-2 and tuberculosis. Conclusions In this South African setting, HIV-1 and tuberculosis are common co-morbidities in patients presenting with COVID-19. In environments in which tuberculosis is common, SARS-CoV-2 and tuberculosis may co-exist with clinical presentation being typical of either disease. Clinical suspicion of exacerbation of co-existent tuberculosis accompanying SARS-CoV-2 should be high. What is already known on this topic? It has been quite widely thought that Africa has been spared the worst effects of the COVID-19 pandemic. There are very few reported case series and no case-control studies comparing COVID-19 patients admitted to hospital to those admitted for other reasons. However several studies have indicated both HIV-1 and tuberculosis co-infection that are endemic in Africa constitute risk factors for poor outcome. In addition Africa is subject to demographic transition and the prevalence of non-communicable co-morbidities such as type 2 diabetes, hypertension and cardiovascular disease is rising rapidly. No study from Africa has described the clinical impact on the presentation of COVID-19 infection. What this study adds Two or more co-morbidities were present in over half COVID-19 presentations, including HIV-1 (30%) and active tuberculosis (14%). Patients dually infected by tuberculosis and SARS-CoV-2, presented as either SARS-CoV-2 or tuberculosis. HIV-1 and SARS-CoV2 co-infection resulted in lower absolute number and proportion of CD4 lymphocytes, and those with low CD4 counts had absent or lower antibody responses against SARS-CoV2. Death occurred 29% of all COVID-19 patients and in 40% of patients with coincident SARS-CoV-2 and tuberculosis. Thus in environments in which tuberculosis is common, SARS-CoV-2 and tuberculosis may co-exist with clinical presentation being typical of either disease and clinical suspicion of exacerbation of co-existent tuberculosis accompanying SARS-CoV-2 should be high. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This research was funded in whole, or in part, by Wellcome [104803, 203135, 222754]. For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. RJW was supported by the Francis Crick Institute which receives its core funding from Cancer Research UK (FC0010218), the UK Medical Research Council (FC0010218), and Wellcome (FC0010218). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The study was approved by the University of Cape Town Health Sciences Research Ethical Committee (HREC 207/2020) All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes Data will be made available following formal publication via contact with the corresponding author","author":[{"propositions":[],"lastnames":["Du Bruyn"],"firstnames":["Elsa"],"suffixes":[]},{"propositions":[],"lastnames":["Stek"],"firstnames":["Cari"],"suffixes":[]},{"propositions":[],"lastnames":["Daroowala"],"firstnames":["Remi"],"suffixes":[]},{"propositions":[],"lastnames":["Said-Hartley"],"firstnames":["Qonita"],"suffixes":[]},{"propositions":[],"lastnames":["Hsiao"],"firstnames":["Marvin"],"suffixes":[]},{"propositions":[],"lastnames":["Goliath"],"firstnames":["Rene","T."],"suffixes":[]},{"propositions":[],"lastnames":["Abrahams"],"firstnames":["Fatima"],"suffixes":[]},{"propositions":[],"lastnames":["Jackson"],"firstnames":["Amanda"],"suffixes":[]},{"propositions":[],"lastnames":["Wasserman"],"firstnames":["Sean"],"suffixes":[]},{"propositions":[],"lastnames":["Allwood"],"firstnames":["Brian","W"],"suffixes":[]},{"propositions":[],"lastnames":["Davis"],"firstnames":["Angharad","G"],"suffixes":[]},{"propositions":[],"lastnames":["Lai"],"firstnames":["Rachel","P-J."],"suffixes":[]},{"propositions":[],"lastnames":["Coussens"],"firstnames":["Anna","K"],"suffixes":[]},{"propositions":[],"lastnames":["Wilkinson"],"firstnames":["Katalin","A"],"suffixes":[]},{"propositions":["de"],"lastnames":["Vries"],"firstnames":["Jantina"],"suffixes":[]},{"propositions":[],"lastnames":["Tiffin"],"firstnames":["Nicki"],"suffixes":[]},{"propositions":[],"lastnames":["Cerrone"],"firstnames":["Maddalena"],"suffixes":[]},{"propositions":[],"lastnames":["Ntusi"],"firstnames":["Ntobeko","A","B"],"suffixes":[]},{"propositions":[],"lastnames":["Riou"],"firstnames":["Catherine"],"suffixes":[]},{"propositions":[],"lastnames":["Wilkinson"],"firstnames":["Robert","J"],"suffixes":[]},{"propositions":[],"lastnames":["Investigators"],"firstnames":["on","behalf","of","the","HIATUS"],"suffixes":[]},{"propositions":[],"lastnames":["Aziz"],"firstnames":["Saalikha"],"suffixes":[]},{"propositions":[],"lastnames":["Bangani"],"firstnames":["Nonzwakazi"],"suffixes":[]},{"propositions":[],"lastnames":["Black"],"firstnames":["John"],"suffixes":[]},{"propositions":[],"lastnames":["Bremer"],"firstnames":["Marise"],"suffixes":[]},{"propositions":[],"lastnames":["Burgers"],"firstnames":["Wendy"],"suffixes":[]},{"propositions":[],"lastnames":["Ciko"],"firstnames":["Zandile"],"suffixes":[]},{"propositions":[],"lastnames":["Esmail"],"firstnames":["Hanif"],"suffixes":[]},{"propositions":[],"lastnames":["Gordon"],"firstnames":["Siamon"],"suffixes":[]},{"propositions":[],"lastnames":["Harley"],"firstnames":["Yolande","X","R"],"suffixes":[]},{"propositions":[],"lastnames":["Lakay"],"firstnames":["Francisco"],"suffixes":[]},{"propositions":[],"lastnames":["Martinez-Estrada"],"firstnames":["Fernando-Oneissi"],"suffixes":[]},{"propositions":[],"lastnames":["Meintjes"],"firstnames":["Graeme","A"],"suffixes":[]},{"propositions":[],"lastnames":["Mendelson"],"firstnames":["Marc"],"suffixes":[]},{"propositions":[],"lastnames":["Papavarnavas"],"firstnames":["Tari"],"suffixes":[]},{"propositions":[],"lastnames":["Proust"],"firstnames":["Alize"],"suffixes":[]},{"propositions":[],"lastnames":["Ruzive"],"firstnames":["Sheena"],"suffixes":[]},{"propositions":[],"lastnames":["Schafer"],"firstnames":["Georgia"],"suffixes":[]},{"propositions":[],"lastnames":["Serole"],"firstnames":["Keboile"],"suffixes":[]},{"propositions":[],"lastnames":["Whitaker"],"firstnames":["Claire"],"suffixes":[]},{"propositions":[],"lastnames":["Zvinairo"],"firstnames":["Kennedy"],"suffixes":[]}],"doi":"10.1101/2021.05.11.21256479","file":":C$\\$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Du Bruyn et al. - 2021 - Communicable and non-communicable co-morbidities and the presentation of COVID-19 in an African setting of high.pdf:pdf","journal":"medRxiv","keywords":"OA,OA_PMC,fund_ack,genomics_fund_ack,original","mendeley-tags":"OA,OA_PMC,fund_ack,genomics_fund_ack,original","month":"may","pages":"2021.05.11.21256479","publisher":"Cold Spring Harbor Laboratory Press","title":"Communicable and non-communicable co-morbidities and the presentation of COVID-19 in an African setting of high HIV-1 and tuberculosis prevalence","url":"https://www.medrxiv.org/content/10.1101/2021.05.11.21256479v1 https://www.medrxiv.org/content/10.1101/2021.05.11.21256479v1.abstract","year":"2021","bibtex":"@article{Bruyn2021,\r\nabstract = {Objectives To describe the presentation and outcome of SARS-CoV2 infection in an African setting of high non-communicable co-morbidity and also HIV-1 and tuberculosis prevalence. Design Case control analysis with cases stratified by HIV-1 and tuberculosis status. Setting A single-centre observational case-control study of adults admitted to a South African hospital with proven SARS-CoV-2 infection or alternative diagnosis. Participants 104 adults with RT-PCR-proven SARS-CoV2 infection of which 55 (52.9{\\%}) were male and 31 (29.8{\\%}) HIV-1 co-infected. 40 adults (35.7{\\%} male, 30.9{\\%} HIV-1 co-infected) admitted during the same period with no RT-PCR or serological evidence of SARS-CoV2 infection and assigned alternative diagnoses. Additional in vitro data from prior studies of 72 healthy controls and 118 HIV-1 uninfected and infected persons participants enrolled to a prior study with either immune evidence of tuberculosis sensitization but no symptoms or microbiologically confirmed pulmonary tuberculosis. Results Two or more co-morbidities were present in 57.7{\\%} of 104 RT-PCR proven COVID-19 presentations, the commonest being hypertension (48{\\%}), type 2 diabetes mellitus (39{\\%}), obesity (31{\\%}) but also HIV-1 (30{\\%}) and active tuberculosis (14{\\%}). Amongst patients dually infected by tuberculosis and SARS-CoV-2, clinical features could be dominated by either SARS-CoV-2 or tuberculosis: lymphopenia was exacerbated, and some markers of inflammation (D-dimer and ferritin) elevated in singly SARS-CoV-2 infected patients were even further elevated (p {\\textless} 0.05). HIV-1 and SARS-CoV2 co-infection resulted in lower absolute number and proportion of CD4 lymphocytes, with those in the lowest peripheral CD4 percentage strata exhibiting absent or lower antibody responses against SARS-CoV2. Death occurred in 30/104 (29{\\%}) of all COVID-19 patients and in 6/15 (40{\\%}) of patients with coincident SARS-CoV-2 and tuberculosis. Conclusions In this South African setting, HIV-1 and tuberculosis are common co-morbidities in patients presenting with COVID-19. In environments in which tuberculosis is common, SARS-CoV-2 and tuberculosis may co-exist with clinical presentation being typical of either disease. Clinical suspicion of exacerbation of co-existent tuberculosis accompanying SARS-CoV-2 should be high. What is already known on this topic? It has been quite widely thought that Africa has been spared the worst effects of the COVID-19 pandemic. There are very few reported case series and no case-control studies comparing COVID-19 patients admitted to hospital to those admitted for other reasons. However several studies have indicated both HIV-1 and tuberculosis co-infection that are endemic in Africa constitute risk factors for poor outcome. In addition Africa is subject to demographic transition and the prevalence of non-communicable co-morbidities such as type 2 diabetes, hypertension and cardiovascular disease is rising rapidly. No study from Africa has described the clinical impact on the presentation of COVID-19 infection. What this study adds Two or more co-morbidities were present in over half COVID-19 presentations, including HIV-1 (30{\\%}) and active tuberculosis (14{\\%}). Patients dually infected by tuberculosis and SARS-CoV-2, presented as either SARS-CoV-2 or tuberculosis. HIV-1 and SARS-CoV2 co-infection resulted in lower absolute number and proportion of CD4 lymphocytes, and those with low CD4 counts had absent or lower antibody responses against SARS-CoV2. Death occurred 29{\\%} of all COVID-19 patients and in 40{\\%} of patients with coincident SARS-CoV-2 and tuberculosis. Thus in environments in which tuberculosis is common, SARS-CoV-2 and tuberculosis may co-exist with clinical presentation being typical of either disease and clinical suspicion of exacerbation of co-existent tuberculosis accompanying SARS-CoV-2 should be high. {\\#}{\\#}{\\#} Competing Interest Statement The authors have declared no competing interest. {\\#}{\\#}{\\#} Funding Statement This research was funded in whole, or in part, by Wellcome [104803, 203135, 222754]. For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. RJW was supported by the Francis Crick Institute which receives its core funding from Cancer Research UK (FC0010218), the UK Medical Research Council (FC0010218), and Wellcome (FC0010218). {\\#}{\\#}{\\#} Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The study was approved by the University of Cape Town Health Sciences Research Ethical Committee (HREC 207/2020) All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes Data will be made available following formal publication via contact with the corresponding author},\r\nauthor = {{Du Bruyn}, Elsa and Stek, Cari and Daroowala, Remi and Said-Hartley, Qonita and Hsiao, Marvin and Goliath, Rene T. and Abrahams, Fatima and Jackson, Amanda and Wasserman, Sean and Allwood, Brian W and Davis, Angharad G and Lai, Rachel P-J. and Coussens, Anna K and Wilkinson, Katalin A and de Vries, Jantina and Tiffin, Nicki and Cerrone, Maddalena and Ntusi, Ntobeko A B and Riou, Catherine and Wilkinson, Robert J and Investigators, on behalf of the HIATUS and Aziz, Saalikha and Bangani, Nonzwakazi and Black, John and Bremer, Marise and Burgers, Wendy and Ciko, Zandile and Esmail, Hanif and Gordon, Siamon and Harley, Yolande X R and Lakay, Francisco and Martinez-Estrada, Fernando-Oneissi and Meintjes, Graeme A and Mendelson, Marc and Papavarnavas, Tari and Proust, Alize and Ruzive, Sheena and Schafer, Georgia and Serole, Keboile and Whitaker, Claire and Zvinairo, Kennedy},\r\ndoi = {10.1101/2021.05.11.21256479},\r\nfile = {:C$\\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Du Bruyn et al. - 2021 - Communicable and non-communicable co-morbidities and the presentation of COVID-19 in an African setting of high.pdf:pdf},\r\njournal = {medRxiv},\r\nkeywords = {OA,OA{\\_}PMC,fund{\\_}ack,genomics{\\_}fund{\\_}ack,original},\r\nmendeley-tags = {OA,OA{\\_}PMC,fund{\\_}ack,genomics{\\_}fund{\\_}ack,original},\r\nmonth = {may},\r\npages = {2021.05.11.21256479},\r\npublisher = {Cold Spring Harbor Laboratory Press},\r\ntitle = {{Communicable and non-communicable co-morbidities and the presentation of COVID-19 in an African setting of high HIV-1 and tuberculosis prevalence}},\r\nurl = {https://www.medrxiv.org/content/10.1101/2021.05.11.21256479v1 https://www.medrxiv.org/content/10.1101/2021.05.11.21256479v1.abstract},\r\nyear = {2021}\r\n}\r\n","author_short":["Du Bruyn, E.","Stek, C.","Daroowala, R.","Said-Hartley, Q.","Hsiao, M.","Goliath, R. 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