The Importation and Establishment of Community Transmission of SARS-CoV-2 During the First Eight Weeks of the South African COVID-19 Epidemic

McCarthy, Kerrigan; Tempia, Stefano; Kufa, Tendesayi; Kleynhans, Jackie; Wolter, Nicole; Jassat, Waasila; Ebonwu, Joy; Gottberg, Anne von; Erasmus, Linda; Muchengeti, Mazvita; Walaza, Sibongile; Ntshoe, Genevie; Shonhiwa, Andronica Moipone; Manana, Pinky N.; Pillay, Yogan; Moonasar, Devanand; Muthivhi, Tshilidzi; Mngemane, Shadrack; Mlisana, Koleka; Chetty, Kamy; Blumberg, Lucille; Cohen, Cheryl; Govender, Nelesh P.; Group, COVID-19 Team

doi:10.2139/ssrn.3792114

Cited by 6 publications

(7 citation statements)

References 9 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…South Africa experienced the first wave 2 months later than did other countries and benefited from time for hospital preparedness and learning from other countries' experiences and the use of steroids, which were shown to improve clinical outcomes. 33 The country was less well prepared for the second wave, which was not predicted to have started as early as it did.…”

Section: Discussionmentioning

confidence: 99%

Difference in mortality among individuals admitted to hospital with COVID-19 during the first and second waves in South Africa: a cohort study

Jassat¹,

Mudara²,

Ozougwu³

et al. 2021

The Lancet Global Health

Self Cite

152

106

View full text Add to dashboard Cite

Background The first wave of COVID-19 in South Africa peaked in July, 2020, and a larger second wave peaked in January, 2021, in which the SARS-CoV-2 501Y.V2 (Beta) lineage predominated. We aimed to compare in-hospital mortality and other patient characteristics between the first and second waves.Methods In this prospective cohort study, we analysed data from the DATCOV national active surveillance system for COVID-19 admissions to hospital from March 5, 2020, to March 27, 2021. The system contained data from all hospitals in South Africa that have admitted a patient with COVID-19. We used incidence risk for admission to hospital and determined cutoff dates to define five wave periods: pre-wave 1, wave 1, post-wave 1, wave 2, and post-wave 2. We compared the characteristics of patients with COVID-19 who were admitted to hospital in wave 1 and wave 2, and risk factors for in-hospital mortality accounting for wave period using random-effect multivariable logistic regression.Findings Peak rates of COVID-19 cases, admissions, and in-hospital deaths in the second wave exceeded rates in the first wave: COVID-19 cases, 240•4 cases per 100 000 people vs 136•0 cases per 100 000 people; admissions, 27•9 admissions per 100 000 people vs 16•1 admissions per 100 000 people; deaths, 8•3 deaths per 100 000 people vs 3•6 deaths per 100 000 people. The weekly average growth rate in hospital admissions was 20% in wave 1 and 43% in wave 2 (ratio of growth rate in wave 2 compared with wave 1 was 1•19, 95% CI 1•18-1•20). Compared with the first wave, individuals admitted to hospital in the second wave were more likely to be age 40-64 years (adjusted odds ratio [aOR] 1•22, 95% CI 1•14-1•31), and older than 65 years (aOR 1•38, 1•25-1•52), compared with younger than 40 years; of Mixed race (aOR 1•21, 1•06-1•38) compared with White race; and admitted in the public sector (aOR 1•65, 1•41-1•92); and less likely to be Black (aOR 0•53, 0•47-0•60) and Indian (aOR 0•77, 0•66-0•91), compared with White; and have a comorbid condition (aOR 0•60, 0•55-0•67).For multivariable analysis, after adjusting for weekly COVID-19 hospital admissions, there was a 31% increased risk of in-hospital mortality in the second wave (aOR 1•31, 95% CI 1•28-1•35). In-hospital case-fatality risk increased from 17•7% in weeks of low admission (<3500 admissions) to 26•9% in weeks of very high admission (>8000 admissions; aOR 1•24, 1•17-1•32).Interpretation In South Africa, the second wave was associated with higher incidence of COVID-19, more rapid increase in admissions to hospital, and increased in-hospital mortality. Although some of the increased mortality can be explained by admissions in the second wave being more likely in older individuals, in the public sector, and by the increased health system pressure, a residual increase in mortality of patients admitted to hospital could be related to the new Beta lineage.

show abstract

Section: Discussionmentioning

confidence: 99%

Difference in mortality among individuals admitted to hospital with COVID-19 during the first and second waves in South Africa: a cohort study

Jassat¹,

Mudara²,

Ozougwu³

et al. 2021

The Lancet Global Health

Self Cite

152

106

View full text Add to dashboard Cite

show abstract

“…The shifts in trend of admissions and deaths between wave 1 and 2 in South Africa could also be explained by the different context of the epidemic when compared to other countries. South Africa experienced the first wave two months later than other countries and benefitted from time for hospital preparedness and learning from other countries' experiences and the use of steroids (34). The country was less well prepared for the second wave which was not predicted to have started as early as it did.…”

Section: Discussionmentioning

confidence: 99%

Increased mortality among individuals hospitalised with COVID-19 during the second wave in South Africa

Jassat

Mudara

Ozougwu

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

Introduction: South Africa experienced its first wave of COVID-19 peaking in mid-July 2020 and a larger second wave peaking in January 2021, in which the SARS-CoV-2 501Y.V2 lineage predominated. We aimed to compare in-hospital mortality and other patient characteristics between the first and second waves of COVID-19. Methods: We analysed data from the DATCOV national active surveillance system for COVID-19 hospitalisations. We defined four wave periods using incidence risk for hospitalisation, pre-wave 1, wave 1, pre-wave 2 and wave 2. We compared the characteristics of hospitalised COVID-19 cases in wave 1 and wave 2, and risk factors for in-hospital mortality accounting for wave period using multivariable logistic regression. Results: Peak rates of COVID-19 cases, admissions and in-hospital deaths in the second wave exceeded the rates in the first wave (138.1 versus 240.1; 16.7 versus 28.9; and 3.3 versus 7.1 respectively per 100,000 persons). The weekly average incidence risk increase in hospitalisation was 22% in wave 1 and 28% in wave 2 [ratio of growth rate in wave two compared to wave one: 1.04, 95% CI 1.04-1.05]. On multivariable analysis, after adjusting for weekly COVID-19 hospital admissions, there was a 20% increased risk of in-hospital mortality in the second wave (adjusted OR 1.2, 95% CI 1.2-1.3). In-hospital case fatality-risk (CFR) increased in weeks of peak hospital occupancy, from 17.9% in weeks of low occupancy (<3,500 admissions) to 29.6% in weeks of very high occupancy (>12,500 admissions) (adjusted OR 1.5, 95% CI 1.4-1.5). Compared to the first wave, individuals hospitalised in the second wave, were more likely to be older, 40-64 years [OR 1.1, 95% CI 1.0-1.1] and ≥65 years [OR 1.1, 95% CI 1.1-1.1] compared to <40 years; and admitted in the public sector [OR 2.2, 95% CI 1.7-2.8]; and less likely to have comorbidities [OR 0.5, 95% CI 0.5-0.5]. Conclusions: In South Africa, the second wave was associated with higher incidence and more rapid increase in hospitalisations, and increased in-hospital mortality. While some of this is explained by increasing pressure on the health system, a residual increase in mortality of hospitalised patients beyond this, could be related to the new lineage 501Y.V2.

show abstract

“…In South Africa, several SARS-CoV-2 lineages with unique mutations were identified during the first wave, and most of these lineages had spread widely before lockdown and travel restrictions were imposed [120]. Rapid transmission also continued in South Africa from imported cases down to the community even during lockdown [121]. South Africa experienced very high mortality during both the first and second waves, but most African countries also had higher second-wave deaths [122].…”

Section: Is South Africa An Outlier?mentioning

confidence: 99%

The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) Pandemic: Are Africa’s Prevalence and Mortality Rates Relatively Low?

Mariam

2022

Advances in Virology

View full text Add to dashboard Cite

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the cause of coronavirus disease 19 (COVID-19), has been rapidly spreading since December 2019, and within a few months, it turned out to be a global pandemic. The disease affects primarily the lungs, but its pathogenesis spreads to other organs as well. However, its mortality rates vary, and in the majority of infected people, there are no serious consequences. Many factors including advanced age, preexisting health conditions, and genetic predispositions are believed to exacerbate outcomes of COVID-19. The virus contains several structural proteins including the spike (S) protein with subunits for binding, fusion, and internalization into host cells following interaction with host cell receptors and proteases (ACE2 and TMPRSS2, respectively) to cause the subsequent pathology. Although the pandemic has spread into all countries, most of Africa is thought of as having relatively less prevalence and mortality. Several hypotheses have been forwarded as reasons for this and include warmer weather conditions, vaccination with BCG (i.e., trained immunity), and previous malaria infection. From genetics or metabolic points of view, it has been proposed that most African populations could be protected to some degree because they lack some genetic susceptibility risk factors or have low-level expression of allelic variants, such as ACE2 and TMPRSS2 that are thought to be involved in increased infection risk or disease severity. The frequency of occurrence of α-1 antitrypsin (an inhibitor of a tissue-degrading protease, thereby protecting target host tissues including the lung) deficiency is also reported to be low in most African populations. More recently, infections in Africa appear to be on the rise. In general, there are few studies on the epidemiology and pathogenesis of the disease in African contexts, and the overall costs and human life losses due to the pandemic in Africa will be determined by all factors and conditions interacting in complex ways.

show abstract

The Importation and Establishment of Community Transmission of SARS-CoV-2 During the First Eight Weeks of the South African COVID-19 Epidemic

Cited by 6 publications

References 9 publications

Difference in mortality among individuals admitted to hospital with COVID-19 during the first and second waves in South Africa: a cohort study

Difference in mortality among individuals admitted to hospital with COVID-19 during the first and second waves in South Africa: a cohort study

Increased mortality among individuals hospitalised with COVID-19 during the second wave in South Africa

The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) Pandemic: Are Africa’s Prevalence and Mortality Rates Relatively Low?

Contact Info

Product

Resources

About