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Salim S. Abdool Karim, FRS
Director: CAPRISA
CAPRISA Professor of Global Health, Columbia University
Co-Chair: Ministerial...
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Expected & actual all-cause deaths during Covid-19
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The fine balance between virus and host
• Viruses usually evolve to become more transmissible & less
severe (less pathogen...
2nd wave – new 501.V2 variant with 3 RBD
mutations has spread & become predominant
3 RBD mutations: K417N, E484K, N501Y
- ...
Preliminary results:
501.V2 variant associated with higher viral load
Speculate the following:
• Higher viral load in swab...
What do & don’t we know about the 501.V2 variant?
1. Unusual for a new variant to contain several mutations – 3 in
RBD inc...
What should we do next?
1. There is reason for concern that we have a virus that seems
to be spreading rapidly; but it is ...
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The 2nd Covid-19 wave in South Africa: Transmissibility & a 501.V2 variant Slide 1 The 2nd Covid-19 wave in South Africa: Transmissibility & a 501.V2 variant Slide 2 The 2nd Covid-19 wave in South Africa: Transmissibility & a 501.V2 variant Slide 3 The 2nd Covid-19 wave in South Africa: Transmissibility & a 501.V2 variant Slide 4 The 2nd Covid-19 wave in South Africa: Transmissibility & a 501.V2 variant Slide 5 The 2nd Covid-19 wave in South Africa: Transmissibility & a 501.V2 variant Slide 6 The 2nd Covid-19 wave in South Africa: Transmissibility & a 501.V2 variant Slide 7 The 2nd Covid-19 wave in South Africa: Transmissibility & a 501.V2 variant Slide 8 The 2nd Covid-19 wave in South Africa: Transmissibility & a 501.V2 variant Slide 9 The 2nd Covid-19 wave in South Africa: Transmissibility & a 501.V2 variant Slide 10 The 2nd Covid-19 wave in South Africa: Transmissibility & a 501.V2 variant Slide 11 The 2nd Covid-19 wave in South Africa: Transmissibility & a 501.V2 variant Slide 12
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The 2nd Covid-19 wave in South Africa: Transmissibility & a 501.V2 variant

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The 2nd Covid-19 wave in South Africa: Transmissibility & a 501.V2 variant

  1. 1. Salim S. Abdool Karim, FRS Director: CAPRISA CAPRISA Professor of Global Health, Columbia University Co-Chair: Ministerial Advisory Committee on COVID-19 Member: African Task Force for Coronavirus Pro Vice-Chancellor (Research): University of KwaZulu-Natal Adjunct Professor in Immunology and Infectious Diseases, Harvard University Adjunct Professor of Medicine: Cornell University The 2nd Covid-19 wave in South Africa: Transmissibility & a 501.V2 variant Ministerial Briefing, 18 December 2020 CAPRISA hosts a MRC HIV-TB Pathogenesis and Treatment Research Unit CAPRISA hosts a DoH-MRC Special Initiative for HIV Prevention TechnologyCAPRISA is the UNAIDS Collaborating Centre for HIV Research and Policy CAPRISA hosts a DST-NRF Centre of Excellence in HIV Prevention
  2. 2. 0 500 1000 1500 2000 2500 3000 3500 0 1000 2000 3000 4000 5000 6000 7000 8000 9000 10000 11000 12000 13000 14000 05-Mar 12-Mar 19-Mar 26-Mar 02-Apr 09-Apr 16-Apr 23-Apr 30-Apr 07-May 14-May 21-May 28-May 04-Jun 11-Jun 18-Jun 25-Jun 02-Jul 09-Jul 16-Jul 23-Jul 30-Jul 06-Aug 13-Aug 20-Aug 27-Aug 03-Sep 10-Sep 17-Sep 24-Sep 01-Oct 08-Oct 15-Oct 22-Oct 29-Oct 05-Nov 12-Nov 19-Nov 26-Nov 03-Dec 10-Dec 17-Dec 7-daymovingaverageofdaily admissionstoDATCOVsentinel hospitalsanddeaths 7-daymovingaverageofdailycases Hospital admissions Cases Deaths Level 5 doubling: 15 days Before lockdown Doubling: 2 days Level 4 doubling: 12 days Level 3 doubling – Jun- 16 Aug: 25 days L2 doubling – 17 Aug – 20 Sept: 206 days L1 doubling – 21 Sept – 28 Nov: 276 days New cases Deaths Hospital Admissions Source of hospital admissions data: Lucille Blumberg and Waasila Jassat – DATCOV, NICD Covid-19 in South Africa 7-day moving average of new cases, sentinel hospital admissions and Covid-19 deaths – to 17 Dec (892,813) (24,011) L1 doubling (start of 2nd wave) – 29 Nov – 16 Dec: 102 days (116,335)
  3. 3. KwaZulu-Natal Gauteng Eastern Cape Western Cape National 0 5 10 15 20 25 30 35 40 45 05-Mar 12-Mar 19-Mar 26-Mar 02-Apr 09-Apr 16-Apr 23-Apr 30-Apr 07-May 14-May 21-May 28-May 04-Jun 11-Jun 18-Jun 25-Jun 02-Jul 09-Jul 16-Jul 23-Jul 30-Jul 06-Aug 13-Aug 20-Aug 27-Aug 03-Sep 10-Sep 17-Sep 24-Sep 01-Oct 08-Oct 15-Oct 22-Oct 29-Oct 05-Nov 12-Nov 19-Nov 26-Nov 03-Dec 10-Dec 17-Dec 7-daymovingaverageofnationaldailycases per100,000population KwaZulu-Natal Gauteng Limpopo Mpumalanga North West Eastern Cape Western Cape Free State Northern Cape National Confirmed SARS-Cov-2 cases by province (7-day moving average cases per 100,000 population – up to 17 December)
  4. 4. 0 1 2 3 4 5 01-Nov 02-Nov 03-Nov 04-Nov 05-Nov 06-Nov 07-Nov 08-Nov 09-Nov 10-Nov 11-Nov 12-Nov 13-Nov 14-Nov 15-Nov 16-Nov 17-Nov 18-Nov 19-Nov 20-Nov 21-Nov 22-Nov 23-Nov 24-Nov 25-Nov 26-Nov 27-Nov 28-Nov 29-Nov 30-Nov 01-Dec 02-Dec 03-Dec 04-Dec 05-Dec 06-Dec 07-Dec 08-Dec 09-Dec 10-Dec 11-Dec 12-Dec 13-Dec 14-Dec 15-Dec 16-Dec 17-Dec 18-Dec 19-Dec 20-Dec 7-daymovingaverageofnationaldailycases per100,000population Limpopo Mpumalanga North West Free State Northern Cape Confirmed SARS-Cov-2 cases by province (7-day moving average cases per 100,000 population – up to 17 December)
  5. 5. 0 5 10 15 20 25 30 35 40 1 5 9 13 17 21 25 29 33 37 41 45 49 53 57 61 65 69 73 77 81 85 89 93 97 101 105 109 113 117 121 125 129 133 137 141 145 149 153 157 161 165 169 173 177 181 185 189 193 197 201 205 7-daymovingaverageofnationaldailycases per100,000population Western Cape - first waveWestern Cape - second wave Comparison of SARS-Cov-2 cases in first and second wave in Western Cape (7-day moving average cases per 100,000 population – up to 17 December) First wave Second wave Latest results: 59/67 (88% are the new variant)
  6. 6. 0 5 10 15 20 25 30 1 5 9 13 17 21 25 29 33 37 41 45 49 53 57 61 65 69 73 77 81 85 89 93 97 101 105 109 113 117 121 125 129 133 137 141 145 149 153 157 161 165 169 173 177 181 185 189 193 197 201 205 209 213 217 7-daymovingaverageofnationaldailycases per100,000population KwaZulu-Natal - first wave KwaZulu-Natal - second wave Comparison of SARS-Cov-2 cases in first and second wave in KwaZulu-Natal (7-day moving average cases per 100,000 population – up to 17 December) First wave Second wave
  7. 7. Expected & actual all-cause deaths during Covid-19 0 2000 4000 6000 8000 10000 12000 14000 16000 18000 04-Mar 11-Mar 18-Mar 25-Mar 01-Apr 08-Apr 15-Apr 22-Apr 29-Apr 06-May 13-May 20-May 27-May 03-Jun 10-Jun 17-Jun 24-Jun 01-Jul 08-Jul 15-Jul 22-Jul 29-Jul 05-Aug 12-Aug 19-Aug 26-Aug 02-Sep 09-Sep 16-Sep 23-Sep 30-Sep 07-Oct 14-Oct 21-Oct 28-Oct 04-Nov 11-Nov 18-Nov 25-Nov 02-Dec 09-Dec 16-Dec Excess deaths COVID-19 deaths Predicted deaths Cases Recorded deaths Before lockdown Excess deaths: 210 Covid-19 deaths : 0 L5 Excess deaths: -3,714 Covid-19 deaths: 93 L4 Excess deaths: -3,894 Covid-19 deaths: 667 L3 – 1 Jun – 16 Aug Excess deaths: 32,809 Covid-19 deaths: 11,483 5 Mar – 31 May: 7,608 less deaths (all-causes) than expected, mostly from fewer non-natural deaths 1 Jun – 16 Aug: 32,809 excess deaths (all-causes) - 11,483 reported Covid-19 deaths National cases L2 - 17 Aug – 20 Sept Excess deaths: 5,132 Covid-19 deaths: 3,854 Source: Bradshaw D, et al L1 - 21 Sept Excess deaths: 12,116 Covid-19 deaths: 6,314
  8. 8. The fine balance between virus and host • Viruses usually evolve to become more transmissible & less severe (less pathogenic or less lethal) • Mostly within humans in response to immune pressure • Sometimes when they pass through another species • SARS-CoV-2 relatively stable in 1st wave – SA recorded about 35 lineages (most were the more transmissible D614G variant from Europe with minor variations) • 2nd wave now in all provinces with some early signs of it spreading faster than 1st wave • Not clear if 2nd wave has more or less deaths (severity unclear)
  9. 9. 2nd wave – new 501.V2 variant with 3 RBD mutations has spread & become predominant 3 RBD mutations: K417N, E484K, N501Y - ↑ affinity to ACE2 receptor & potential Ab escape Probably originated in NMB – spread to EC, Garden route, KZN & Cape Town Source: Tyler N et al, Cell 2020
  10. 10. Preliminary results: 501.V2 variant associated with higher viral load Speculate the following: • Higher viral load in swabs may translate to higher efficiency of transmission ie. Higher transmissibility • This may translate into a higher R0 • While other viruses are transmitting, this variant is transmitting faster • This may translate into a 2nd wave that will have many more cases than 1st wave
  11. 11. What do & don’t we know about the 501.V2 variant? 1. Unusual for a new variant to contain several mutations – 3 in RBD incl. N501Y – which alters ACE2 affinity & ?Ab effects 2. N501Y is being reported in other countries (0.2%) e.g. UK 3. Early signs that the new variant is spreading fast – sometimes faster than 1st wave viruses 4. It is widespread – probably across most of SA by now 1. Where did it come from & why did it form? Why NMB? – we have a few hypotheses to investigate 2. Is it more severe? – to early to tell 3. Is it re-infecting people who got infected in the 1st wave 4. Will the current vaccines work against this variant? – currently being studied by KRISP, AHRI, NICD & CAPRISA
  12. 12. What should we do next? 1. There is reason for concern that we have a virus that seems to be spreading rapidly; but it is something we can deal with. 2. Same prevention measures & treatment work for 501.V2 3. Similar 501 variants are in other countries e.g. Australia, UK 4. Inform key role-players & the public about the 501.V2 variant 5. Publish the data in a prominent journal 6. Urgently increase phylogenetic screening – need to sequence 100-200 viruses every month from across SA 7. Complete the studies to answer the 4 unknowns – fortunately, there are vaccine trials underway in SA e.g. J&J

The 2nd Covid-19 wave in South Africa: Transmissibility & a 501.V2 variant

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