New COVID-19 variant identified in SA

Health Minister Dr Zweli Mkhize on Friday announced that a variant of the SARS-COV-2 Virus (COVID-19) – currently termed the ‘501.V2 Variant’ –  has been identified by genomics scientists in South Africa.

Mkhize said a genomics team, led by the Kwazulu-Natal Research Innovation and Sequencing Platform, or KRISP, has sequenced hundreds of samples from across the country since the beginning of the pandemic in March. They noticed that a particular variant has increasingly dominated the findings of the samples collected in the past two months.

In addition, clinicians have been providing anecdotal evidence of a shift in the clinical epidemiological picture- in particular noting that they are seeing a larger proportion of younger patients with no co-morbidities presenting with critical illness. The evidence that has been collated, therefore, strongly suggests that that the current second wave we are experiencing is being driven by this new variant.

Explaining the findings, Professor Salim Abdool Karim said the second wave is showing some early signs that it is spreading faster than the first wave.

“It is still very early but at this stage, the preliminary data suggests that the virus that is now dominating in the second wave is spreading faster than the first wave. It is not clear if the second wave has more or less deaths, in other words, the severity is still very unclear. We would expect it to be a less severe virus, but we do not have clear evidence at this point. We have not seen any red flags looking at our current death information,” he said.

“We had all of these different strains routinely spreading in South Africa during our first wave and subsequently. What became quite different that we did not expect is the rapid way in which this variant has become dominant in South Africa.

This particular virus has three mutations on the receptor-binding domain, which is the actual part of the virus that attaches to the human cell. One of the interpretations of these changes is that it increases the affinity for the ACE2 receptor. The other two mutations possible add some potential antibody escape but the full implications of the combination of the three mutations still need to be understood in more detail.”

Karim said the new variant has increased viral loads in the body.

“When we look at this new variant, the CT score is lower than the other viruses that have been spreading during our first wave. It means that the amount of virus in the swab is higher. A lower score means a higher amount of virus: we refer to that as the viral load. When we do a swab, we are getting a lot more virus in these patients that have the 501.V2 virus,” he said.

“The higher viral load in these swabs may translate to a higher efficiency of transmission. If there’s higher transmissibility, it may translate to a higher R0 (the number of additional people one patient may infect). While the other viruses are still transmitting, this virus is spreading so much faster that when we take swabs it is the dominant variant that we see. This may translate into a second wave that may have many more cases than the first wave.

We do know that it is an unusual variant. It has been reported in other countries, including the UK, Australia and several others. In our country, we are finding between 80 and 90% of the virus is this 501.V2 mutant.”

He said there are still many issues that need to be investigated.

“We don’t know where it came from and we don’t know why it formed. We found the first in Nelson Mandela Bay, but we don’t know if it originated in Nelson Mandela Bay. It is too early to tell if it is more severe.”

Concluding the briefing, Mkhize said that while this mutation is a cause for concern, there is no reason to panic.

“We appeal to all the media and medical and scientific community to focus on the facts and avoid entering into speculation or issue unproven statements and generate panic and disinformation. This research underlines the need for all of us all to loyally adhere to the practice of non-pharmaceutical interventions which work as effectively in any pandemic of this nature including COVID-19 as we have known it and is just as effective to a mutant variant of the same virus,” he said.

“Nothing will beat the rigid implementation of wearing of masks, use of hand sanitizer and washing with soap and distancing. Many countries experienced a second wave that was more severe than first – even where no mutations were reported.

He said there is no evidence to suggest a need to change in clinical treatment and patient management of COVID-19 in the second wave to date and that this discovery does not necessitate additional restrictive measures.

Issued by the Department of Health, 18 December 2020

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Update on Covid-19 (18th December 2020)

18 December 2020

Today the cumulative number of cases stands at 901 538 with 8 725 new cases identified since the last report.

A cumulative total of 6 051 986 tests have been completed with 40 751 new tests conducted since the last report.

Regrettably, 274 more COVID-19 related deaths have been reported: Eastern Cape 92 , Free State 6, Gauteng 15, Kwa-Zulu Natal 56, Mpumalanga 4 and Western Cape 101.

This brings the total deaths to 24 285 deaths

We convey our condolences to the loved ones of the departed and thank the health workers that treated the deceased.

Our recoveries now stand at 783 818.

Statement on the 501.V2 Variant

This evening we convened a public briefing to announce that a variant of the SARS-COV-2 Virus-currently termed 501.V2 Variant, has been identified by our genomics scientists here in South Africa.

This genomics team, led by the Kwazulu-Natal Research Innovation and Sequencing Platform, or KRISP, has sequenced hundreds of samples from across the country since the beginning of the pan-demic in March. As they will elaborate shortly, they noticed that a particular variant has increasingly dominated the findings of the samples collected in the past two months. In addition, clinicians have been providing anecdotal evidence of a shift in the clinical epidemiological picture- in particular noting that they are seeing a larger proportion of younger patients with no co-morbidities presenting with crit-ical illness. The evidence that has been collated, therefore, strongly suggests that that the current second wave we are experiencing is being driven by this new variant.

The team at KRISP, led by Professor Tulio de Oliviera, (who will shortly give a presentation) have been sharing their findings with the World Health Organization and the scientific community at large. In fact it was this consortium that alerted the UK to our variant, upon which the UK then studied their own samples and found that a similar mutation on the same site (that is the 501 site), was the variant that was driving their resurgence in London, leading to an announcement being made in Parliament and the lockdown that was instituted in London to curb the spread of this variant. This is the calibre of our own scientists here in South Africa and we are extremely proud to once again demonstrate lead-ership in the COVID-19 response on a world stage.

There are some concerning issues that I wish to bring to the attention of the public:

1. We did not expect the second wave to emerge as soon as it has

2. The second wave has come during the festive season

3. Complacency has set in and people have grown tired of adhering to non-pharmaceutical inter-ventions

However, It is important to reiterate that while this mutation is a cause for concern, there is no reason to panic.

We appeal to all the media and medical and scientific community to focus on the facts and avoid en-tering into speculation or issue unproven statements and generate panic and disinformation

This research underlines the need for all of us all to loyally adhere to the practice of Non pharmaceu-tical interventions which work as effectively in any pandemic of this nature including COVID-19 as we have known it and is just as effective to a mutant variant of the same virus

Nothing will beat the rigid implementation of wearing of masks use of hand sanitizer and washing with soap and distancing

Many countries experienced a second wave that was more severe than first -even where no muta-tions were reported

Our current case management is guided by clinical manifestations of the pandemic and this has still been effective irrespective of the mutation that has been identified.

There is no evidence to suggest a need to change in clinical treatment and patient management of COVID 19 in the second wave to date. I have directed that the clinicians subcommittee of MAC should monitor the situation and issue an advisory whenever the need for changing clinical treatment and patient management is deemed necessary.

We have recently announced more restrictions using a differentiated approach across the country-that is we implemented different containment measures depending on the infection spread such as hotspots and anticipated social behaviour during festive season, as well as strengthening the effec-tiveness of our inspections and enforcement measures.

This discovery does not necessitate additional measures. There will be no basis to change purely based on this report.

Reports based on surveillance and intensive monitoring continues to guide our response which is dri-ven by science. We will declare new districts as hotspots as they reach the threshold and continue to monitor how these increases impact on our health service and health care workers.

In response to the second wave we have directed that all provinces reactivate their resurgence plans and mount the appropriate response to the resurgence of COVID-19 by ensuring

- adequate Human Resources for health: employment of nurses and doctors and all staff that is needed

- reactivation of the field hospital beds

- preparing more ICU beds as in the earlier surge

- provision of adequate oxygen and oxygen delivery tools

We will also ensure adequate psychosocial support for health care workers and they will be prioritised for vaccinations against COVID-19.

Invariably the research raises more questions and I have directed that more work to be done to clarify the following:

- Implications on individuals previously infected and recovered to ascertain if they would be reinfect-ed by the variant- we currently have no information and we must avoid speculation but wait for re-search

- There will also be further research to ascertain if the current vaccines be effective on the new vari-ant- we shall continue with the vaccine program as there is no evidence to do otherwise and scientific research will clarify that. Before that happens there is no new action needed and no evidence to change the approach.

I must take this opportunity to speak to our youth. Last week I made an announcement that we have entered into our second wave and that it is mostly young people who are testing positive for COVID-19 in recent weeks: this continues to be the case. Our clinicians have also warned us that things have changed and that younger, previously healthy people are now becoming very sick.

De-spite all these warnings in the past couple of weeks, we continue to see recent videos on social media of youth partying in large numbers, even some playing kissing games during these parties. Our youth are not wearing masks and are clearly so intoxicated that they have thrown caution to the wind and do not care to observe the rules under the state of disaster. It cannot be that our youth can only adhere to lifesaving measures by being policed.

We call on parents, caregivers and our youth to understand that this is now not just a matter of thinking about others but you yourselves are now equally at risk of dying from COVID-19. We cannot go through what we went through in the early days of the AIDS pandemic when mothers and grandmothers were burying their children- this is the most heartbreaking phenomenon. The youth is urged to take care and find alternative ways of having safe fun this festive season.

The situation can be contained and it all depends on our ability and commitment to change behaviour.

We will continue to update and keep the public informed on any further developments.

Dr Zwelini Mkhize

Minister of Health

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Previous:

Update on Covid-19 (17th December 2020)

Dec 17th, 2020

Today the cumulative number of cases stands at 892 813

A cumulative total of 6 011 235 tests have been completed with 42 543 new tests conducted since the last report.

Regrettably, In the last 24 hours, 184 deaths have been reported: Eastern Cape 103 , Free State 4, Gauteng 11, Kwa-Zulu Natal 8 and Western Cape 58. This brings the total deaths to 24 011.

We convey our condolences to the loved ones of the departed and thank the health workers that treated the deceased.

Our recoveries now stand at 780 313.

Dr Zwelini Mkhize

Minister of Health

Issued by the Department of Health, 17 and 18 December 2020