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

30 Pages Posted: 26 Feb 2021

See all articles by Kerrigan Mccarthy

Kerrigan Mccarthy

National Health Laboratory Services (NHLS) - National Institute for Communicable Diseases

Stefano Tempia

Government of the United States of America - Division of Influenza; Government of the United States of America - Influenza Program; National Health Laboratory Services (NHLS) - Centre for Respiratory Diseases and Meningitis

Tendesayi Kufa

National Health Laboratory Services (NHLS) - National Institute for Communicable Diseases

Jackie Kleynhans

Centre for Respiratory Disease and Meningitis, National Institute for Communicable Diseases

Nicole Wolter

National Health Laboratory Services (NHLS) - Centre for Respiratory Diseases and Meningitis; University of the Witwatersrand - School of Pathology

Waasila Jassat

National Health Laboratory Services (NHLS) - National Institute for Communicable Diseases

Joy Ebonwu

National Health Laboratory Services (NHLS) - National Institute for Communicable Diseases

Anne von Gottberg

National Health Laboratory Services - Centre for Respiratory Diseases and Meningitis; University of the Witwatersrand - School of Pathology

Linda Erasmus

Division of Public Health Surveillance and Response, National Health Laboratory Services (NHLS)

Mazvita Muchengeti

National Cancer Registry, National Health Laboratory Services (NHLS)

Sibongile Walaza

National Health Laboratory Services (NHLS) - Centre for Respiratory Diseases and Meningitis; University of the Witwatersrand - School of Public Health

Genevie Ntshoe

Division of Public Health Surveillance and Response, National Health Laboratory Services (NHLS)

Andronica M. Shonhiwa

Division of Public Health Surveillance and Response, National Health Laboratory Services (NHLS)

Pinky N. Manana

Centre for Emerging, Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases

Yogan Pillay

Clinton Health Access Initiative (CHAI)

Devanand Moonasar

South African Government - National Department of Health

Tshilidzi Muthivhi

National Health Laboratory Services (NHLS) - National Institute for Communicable Diseases

Shadrack Mngemane

Clinton Health Access Initiative (CHAI)

Koleka Mlisana

National Health Laboratory Services (NHLS)

Kamy Chetty

National Health Laboratory Services (NHLS)

Lucille Blumberg

National Health Laboratory Services (NHLS) - National Institute for Communicable Diseases

Cheryl Cohen

National Health Laboratory Services (NHLS) - Centre for Respiratory Diseases and Meningitis; University of the Witwatersrand - School of Public Health

Nelesh P. Govender

University of the Witwatersrand

COVID-19 Team Group

More...

Abstract

Background: We describe the epidemiology of COVID-19 in South Africa following importation and during implementation of stringent lockdown measures.

Methods: Using national surveillance data including demographics, laboratory test data, clinical presentation, risk exposures (travel history, contacts and occupation) and outcomes of persons undergoing COVID-19 testing or hospitalised with COVID-19 at sentinel surveillance sites, we generated and interpreted descriptive statistics, epidemic curves, and initial reproductive numbers (Rt).

Findings: From 4 March to 30 April 2020, 271,670 SARS-CoV-2 PCR tests were performed (462 tests/100,000 persons). Of these, 7,892 (2.9%) persons tested positive (median age 37 years (interquartile range 28-49 years), 4,568 (58%) male, cumulative incidence of 13.4 cases/100,000 persons). Hospitalization records were found for 1,271 patients (692 females (54%)) of whom 186 (14.6%) died. Amongst 2,819 cases with data, 489/2819 (17.3%) travelled internationally within 14 days prior to diagnosis, mostly during March 2020 (466 (95%)). Cases diagnosed in April compared with March were younger (median age, 37 vs. 40 years), less likely female (38% vs. 53%) and resident in a more populous province (98% vs. 91%). The national initial Rt was 2.08 (95% confidence interval (CI): 1.71-2.51).

Interpretation: The first eight weeks following COVID-19 importation were characterised by early predominance of imported cases and relatively low mortality and transmission rates. Despite stringent lockdown measures, the second month following importation was characterised by community transmission and increasing disease burden in more populous provinces.

Funding Statement: South African National and provincial health departments.

Declaration of Interests: We declare no competing interests.

Ethics Approval Statement: Surveillance activities for NMC including SARS-COV-2 infection are conducted by the NICD according to National Health Act Regulations. Publication of surveillance data in the peer-reviewed literature was approved by the University of the Witwatersrand Human Research Ethics Committee (Medical) protocol M160667.

Suggested Citation

Mccarthy, Kerrigan and Tempia, Stefano and Kufa, Tendesayi and Kleynhans, Jackie and Wolter, Nicole and Jassat, Waasila and Ebonwu, Joy and von Gottberg, Anne and Erasmus, Linda and Muchengeti, Mazvita and Walaza, Sibongile and Ntshoe, Genevie and Shonhiwa, Andronica M. and Manana, Pinky N. and Pillay, Yogan and Moonasar, Devanand and Muthivhi, Tshilidzi and Mngemane, Shadrack and Mlisana, Koleka and Chetty, Kamy and Blumberg, Lucille and Cohen, Cheryl and Govender, Nelesh P. and Group, COVID-19 Team, The Importation and Establishment of Community Transmission of SARS-CoV-2 During the First Eight Weeks of the South African COVID-19 Epidemic. Available at SSRN: https://ssrn.com/abstract=3792114 or http://dx.doi.org/10.2139/ssrn.3792114

Kerrigan Mccarthy (Contact Author)

National Health Laboratory Services (NHLS) - National Institute for Communicable Diseases

Johannesburg
South Africa

Stefano Tempia

Government of the United States of America - Division of Influenza ( email )

Atlanta, GA
United States

Government of the United States of America - Influenza Program

Pretoria
South Africa

National Health Laboratory Services (NHLS) - Centre for Respiratory Diseases and Meningitis

Johannesburg
South Africa

Tendesayi Kufa

National Health Laboratory Services (NHLS) - National Institute for Communicable Diseases

Johannesburg
South Africa

Jackie Kleynhans

Centre for Respiratory Disease and Meningitis, National Institute for Communicable Diseases ( email )

Johannesburg
South Africa

Nicole Wolter

National Health Laboratory Services (NHLS) - Centre for Respiratory Diseases and Meningitis

Johannesburg
South Africa

University of the Witwatersrand - School of Pathology

Johannesburg, 2000
South Africa

Waasila Jassat

National Health Laboratory Services (NHLS) - National Institute for Communicable Diseases

Johannesburg
South Africa

Joy Ebonwu

National Health Laboratory Services (NHLS) - National Institute for Communicable Diseases

Johannesburg
South Africa

Anne Von Gottberg

National Health Laboratory Services - Centre for Respiratory Diseases and Meningitis

Johannesburg
South Africa

University of the Witwatersrand - School of Pathology

Johannesburg, 2000
South Africa

Linda Erasmus

Division of Public Health Surveillance and Response, National Health Laboratory Services (NHLS) ( email )

Johannesburg
South Africa

Mazvita Muchengeti

National Cancer Registry, National Health Laboratory Services (NHLS) ( email )

Johannesburg
South Africa

Sibongile Walaza

National Health Laboratory Services (NHLS) - Centre for Respiratory Diseases and Meningitis

Johannesburg
South Africa

University of the Witwatersrand - School of Public Health

Johannesburg
South Africa

Genevie Ntshoe

Division of Public Health Surveillance and Response, National Health Laboratory Services (NHLS) ( email )

Johannesburg
South Africa

Andronica M. Shonhiwa

Division of Public Health Surveillance and Response, National Health Laboratory Services (NHLS) ( email )

Modderfontein Road
Sandringham, Johannesburg
South Africa

Pinky N. Manana

Centre for Emerging, Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases ( email )

Johannesburg
South Africa

Yogan Pillay

Clinton Health Access Initiative (CHAI) ( email )

383 Dorchester Ave
Boston, MA 02127
United States

Devanand Moonasar

South African Government - National Department of Health ( email )

Pretoria
South Africa

Tshilidzi Muthivhi

National Health Laboratory Services (NHLS) - National Institute for Communicable Diseases ( email )

Johannesburg
South Africa

Shadrack Mngemane

Clinton Health Access Initiative (CHAI) ( email )

383 Dorchester Ave
Boston, MA 02127
United States

Koleka Mlisana

National Health Laboratory Services (NHLS) ( email )

Modderfontein Road
Sandringham, Johannesburg
South Africa

Kamy Chetty

National Health Laboratory Services (NHLS) ( email )

Modderfontein Road
Sandringham, Johannesburg
South Africa

Lucille Blumberg

National Health Laboratory Services (NHLS) - National Institute for Communicable Diseases

Johannesburg
South Africa

Cheryl Cohen

National Health Laboratory Services (NHLS) - Centre for Respiratory Diseases and Meningitis ( email )

Johannesburg
South Africa

University of the Witwatersrand - School of Public Health

Johannesburg
South Africa

Nelesh P. Govender

University of the Witwatersrand

1 Jan Smuts Avenue
Johannesburg, GA 2000
South Africa

No contact information is available for COVID-19 Team Group

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