We acknowledge all NGS-SA members and laboratory teams, laboratory teams at the Centre for Respiratory Diseases and Meningitis and the Sequencing Core Facility of the NICD (Johannesburg, South Africa) for genomic sequencing data; and the national SARS-CoV-2 NICD surveillance team and NICD Information Technology team for NMCSS case data. We thank all laboratories for submitting specimens for sequencing, all public and private laboratories for COVID-19 diagnostic test data, and all public laboratories and Lancet Laboratories for ThermoFisher TaqPath™ COVID-19 PCR data. We thank all hospitals and health-care workers submitting data through the DATCOV surveillance programme.
This study was funded by the South African Medical Research Council with funds received from the National Department of Health. Sequencing activities for NICD are supported by a conditional grant from the South African National Department of Health as part of the emergency COVID-19 response; a cooperative agreement between the National Institute for Communicable Diseases of the National Health Laboratory Service and the United States Centers for Disease Control and Prevention (grant number 5 U01IP001048-05-00); the African Society of Laboratory Medicine (ASLM) and Africa Centers for Disease Control and Prevention through a sub-award from the Bill and Melinda Gates Foundation grant number INV-018978; the UK Foreign, Commonwealth and Development Office and Wellcome (Grant no 221003/Z/20/Z); and the UK Department of Health and Social Care and managed by the Fleming Fund and performed under the auspices of the SEQAFRICA project. The Fleming Fund is a £265 million UK aid programme supporting up to 24 low- and middle-income countries (LMICs) generate, share and use data on antimicrobial resistance (AMR) and works in partnership with Mott MacDonald, the Management Agent for the Country and Regional Grants and Fellowship Programme. This research was also supported by The Coronavirus Aid, Relief, and Economic Security Act (CARES ACT) through the Centers for Disease Control and Prevention (CDC) and the COVID International Task Force (ITF) funds through the CDC under the terms of a subcontract with the African Field Epidemiology Network (AFENET) AF-NICD-001/2021. Screening for SGTF at UCT was supported by the Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), which is supported by core funding from the Wellcome Trust (203135/Z/16/Z and 222754).
The findings and conclusions in this manuscript are those of the author(s) and do not necessarily represent the official position of the funding agencies.
The funders played no role in the writing of the manuscript or the decision to submit for publication.
DECLARATION OF INTERESTS
CC has received grant support from South African Medical Research Council, UK Foreign, Commonwealth and Development Office and Wellcome Trust, US Centers for Disease Control and Prevention and Sanofi Pasteur. NW has received grant support from Sanofi Pasteur and the Bill and Melinda Gates Foundation. AvG has received grant support from US Centers for Disease Control and Prevention, Africa Centres for Disease Control and Prevention, African Society for Laboratory Medicine (ASLM), South African Medical Research Council, WHO AFRO, The Fleming Fund and Wellcome Trust. RW declares personal shareholding in the following companies: Adcock Ingram Holdings Ltd, Dischem Pharmacies Ltd, Discovery Ltd, Netcare Ltd, Aspen Pharmacare Holdings Ltd. All other authors declare no conflict of interest.
DATA SHARING STATEMENT
Data used in this manuscript are available upon reasonable request. Proposals should be directed to [email protected].
Conception and design of study: NW, WJ, SW, AvG, CC
Data collection and laboratory processing: NW, WJ, SW, RW, HM, DGA, JE, JNB, CS, NT, NC, MdP, NG, AI, AG, KM, WS, FKT, KS, ZM, NH, RP, JW, AvG, CC
Analysis and interpretation: NW, WJ, SW, RW, HM, MG, DGA, JE, JNB, CS, NC, MdP, NG, AI, AG, KM, WS, FKT, ZM, NH, RP, JW, HH, MD, AB AvG, CC
Accessed and verified the underlying data: NW, RW, HM, DGA, JE, AvG
Drafted the Article: NW, AvG, CC
All authors critically reviewed the Article.