Africa - Coronavirus COVID-19

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Between 83,000 and 190,000 people could die of COVID-19 in Africa, with 29 million to 44 million infected, in the coronavirus pandemic’s first year if containment measures do not work, the African regional office of the World Health Organization said Thursday.

“This is largely driven by social and environmental factors slowing the transmission, and a younger population that has benefited from the control of communicable diseases such as HIV and tuberculosis to reduce possible vulnerabilities,” the WHO said.

As of Thursday, 52 countries in Africa had seen cases, according to WHO Africa’s tally, with 51,239 cases in Africa as a whole and 34,338 cases in the WHO Africa Region, the global health body said. Of those, 17,471 had recovered and 1,926 had died. South Africa remained the most affected, with 7,808 cases, WHO said.
...
“While COVID-19 likely won’t spread as exponentially in Africa as it has elsewhere in the world, it likely will smolder in transmission hotspots,” WHO Regional Director for Africa Matshidiso Moeti said in the agency’s statement. “COVID-19 could become a fixture in our lives for the next several years unless a proactive approach is taken by many governments in the region. We need to test, trace, isolate and treat.”
Up to 190,000 coronavirus deaths possible in Africa in first year of pandemic unless there’s containment, WHO says
 
Africa:

Africa crosses 2.5 million COVID-19 cases - Reuters tally

After COVID, Africa needs to make healthcare a priority

—-

South Africa:

South Africa’s second coronavirus wave is fueled by a new strain, teen ‘rage festivals’

Coronavirus in South Africa: Unravelling the mystery

BBM by me in red / I wonder how correct this article is wrt increased severity:

Severe COVID variant detected in South Africa, health minister says

“JOHANNESBURG, South Africa — A severe variant of the coronavirus has been detected in South Africa which could explain the rapid spread of a second wave that affects younger people, the health minister said Friday.

Known as the 501.V2 Variant, it was identified by South African researchers and details have been sent to the World Health Organization, Zwelini Mkhize said in a statement.“

[...]

“South African doctors have remarked that more patients are younger, and do not always have other conditions that amplify the virus’ effect, but are nonetheless suffering from more severe forms of COVID-19.”

The research team, led by Tulio de Oliveira, has shared its findings with the scientific community and alerted authorities in Britain, who have “studied their own samples and found that a similar mutation… was the variant that was driving their resurgence in London,” he said.”
—

Eta:

Here’s what you need to know about the new coronavirus variant, now confirmed in SA
Dec. 18, 2020

South Africa announces a new coronavirus variant.
Dec. 18, 2020

South Africa identifies new coronavirus strain causing surge in cases
Dec. 18, 2020

““The evidence that has been collated, therefore, strongly suggests that the current second wave we are experiencing is being driven by this new variant,” Mkhize added.

South Africa has recorded the highest number of coronavirus infections in Africa, approaching the 900,000 mark, with over 20,000 related deaths. A resurgence in cases saw the government tighten restrictions on society this week.”

[...]

““We are working with them with our SARS-COV-2 Virus evolution working group. They are growing the virus in the country and they’re working with researchers to determine any changes in the behaviour of the virus itself in terms of transmission,” WHO epidemiologist Maria Van Kerkhove told a news conference in Geneva.“


Why scientists are concerned about SA's 'unusual’ new coronavirus variant | News24
Dec. 19, 2020

* note: the above article contradicts the previous bolded snippets in red, saying the new variant is not more severe.

—

New Variant of SARS-CoV-2 Frequently Asked Questions - NICD
Dec. 19, 2020

“Q What is the new SARS-CoV-2 variant?
A This new variant of the virus was discovered through routine genomic surveillance of SARS-
CoV-2 performed by a network of laboratories around the country (Network for Genomic Surveillance South Africa, NGS-SA). The new variant has been identified in almost 200 samples collected from over 50 different health facilities in Eastern Cape, Western Cape and KwaZulu- Natal. The new variant is different from the others that were circulating in South Africa because it has multiple mutations (changes) in the spike protein – this is the very important part of the virus that binds to the receptor on the cells inside our body and that is also the main target for many of the antibodies produced during infection or after vaccination. Work is being done to understand what effect these mutations have on the behaviour of the virus and our body’s response to it - particularly whether it makes the virus spread more easily, whether it might lead to more severe COVID-19, and whether the virus can evade our immune response.

Q What is the geographical distribution of this mutation?
A The variant was first identified in Nelson Mandela Bay but has rapidly spread through the rest
of the Eastern Cape and to the Western Cape and KwaZulu-Natal provinces. Testing in other provinces is being undertaken to understand the extent of geographical spread but it is likely that this variant has spread to other provinces too.

Q Is the new variant associated with an increase in the severity of the disease?
A At this stage, there is no clear evidence of the new variant being associated with more severe
disease or worse outcomes but clinicians are undertaking more studies to establish if this new variant does change the course of the disease.

Q Is this the same or different to the London variant?
A It is definitely not the same variant, but there are similarities as they both share the same
change in the spike protein at the 501 position. What it does tell us is that if we do not control the spread of the virus then it is likely to evolve in similar ways in different parts of the world.

Q The new variant of infection leads is associated with a higher viral load. Does this mean a higher rate of transmission?
A We do not know for sure that it is associated with a higher viral load, but some of our findings
suggest that might be the case. We need to gather more information to help us understand this. Overall there is some evidence that this new variant might be being transmitted more readily than other variants, although the mechanism of this remains to be fully worked out.”

[...]

“Q Will the new variant cause different symptoms?
A There is no reason to think the types of symptoms you get will be different. Patients will in all likelihood present with the same spectrum of symptoms as before. Whether the overall severity will be different, remains to be seen.”

[...]

“Q Will the new variant have an impact on the effectiveness of vaccines? (1)
A It is not currently known whether or not this mutation will impact on the effectiveness of vaccines.
More research is needed to see whether or not this is the case, and in the event that the mutation significantly reduces vaccine efficacy further vaccine development will be required.“

-more at link
—

@DrZweliMkhize
Dec 18
Karim: This new 501.V2 variant has become dominant in South Africa. This new variant has 3 mutations. #SARSCOV2MediaBriefing

https://mobile.twitter.com/drzwelimkhize/status/1339976270839504905?lang=en
 
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Per this video, “doctors are reporting more young people who are seriously ill”; also, per Hancock, this new South Africa variant is highly concerning because it appears to have mutated further than the one discovered in the UK.
 
(courtesy via @Cool Cats)

Another new coronavirus variant found in Nigeria, says Africa CDC

NAIROBI (Reuters) -Another new variant of the novel coronavirus seems to have emerged in Nigeria, the head of Africa's disease control body said on Thursday, cautioning more investigation was needed.

The news comes after Britain and South Africa both reported new variants of the SARS-CoV-2 virus that appear to be more contagious, leading to new travel restrictions and turmoil in markets.

"It's a separate lineage from the UK and the South African lineages," John Nkengasong, director of the Africa Centres for Disease Control and Prevention (CDC) told an online news conference from Addis Ababa.
 
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Coronavirus Disease 2019 (COVID-19)
Latest updates on the COVID-19 crisis from Africa CDC.
Africa CDC - COVID-19 Daily Updates

“Scientists are still learning about the disease, and think that the virus began in animals. At some point, one or more humans acquired infection from an animal, and those infected humans began transmitting infection to other humans.
The disease spreads from person to person through infected air droplets that are projected during sneezing or coughing. It can also be transmitted when humans have contact with hands or surfaces that contain the virus and touch their eyes, nose, or mouth with the contaminated hands.

COVID-19 was first reported in China, but it has now spread throughout the world.“


Africa CDC Dashboard | Region | All

Cases
2,597,090

Deaths
61,432

Recoveries
2,177,981
 
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Statement on new SARS-CoV-2 variant with multiple spike protein mutations – Africa CDC
22 DECEMBER 2020

“ADDIS ABABA, ETHIOPIA, 22 DECEMBER 2020. The Africa Centres for Disease Control and Prevention (Africa CDC) wishes to raise awareness of Member States regarding the new variant of SARS-CoV-2, the virus that causes COVID-19, which was reported in South Africa and the United Kingdom over the past week. Africa CDC is closely following up with authorities in South Africa, where the variant was first identified in Nelson Mandela Bay and has rapidly spread through the Eastern and Western Capes, as well as KwaZulu-Natal.

This new variant is defined by multiple non-synonymous mutations in the spike (S) protein. Three of these mutations are located on the receptor-binding domain (RBD) of the spike protein – the most notable being the N501Y mutation on the receptor binding motif that binds to the human Angiotensin Converting Enzyme-2 (ACE2) receptor.

Preliminary analyses from South Africa and the United Kingdom suggest that this new variant may be associated with increased transmissibility and a higher viral load than the previously circulating variants.

However, researchers are conducting further investigations on this new N501Y variant to determine if it is more infectious, more transmissible, or has the potential to cause more severe illness. Research is also being conducted to assess the impact of the mutations on the performance of existing molecular diagnostics, serological assays, therapeutics, and vaccines.“
 
Statement on new SARS-CoV-2 variant with multiple spike protein mutations – Africa CDC
22 DECEMBER 2020


“On 21 December, Africa CDC convened an emergency meeting of the Africa Taskforce on Coronavirus Response (AFTCOR), where the Network for Genomics Surveillance in South Africa, led by Prof. Tulio de Olivera and Prof. Salim Abdool Karim, shared findings from South Africa. The meeting discussed what is known, what is not known, and what needs to be done about this new variant. The Taskforce recommends the following:

  • Africa CDC Institute for Pathogen Genomics (IPG) should immediately coordinate further actions by a continental network of clinical laboratory centres of excellence to enhance surveillance of the new variant virus.
  • Member States should enhance implementation of ongoing public health and social measures to prevent further transmission of COVID-19, including correct and consistent mask-wearing, physical distancing and hand hygiene.
  • There is no immediate need to restrict trade and travel across the continent, because travellers across the continent now require a negative virologic test (PCR or Antigen test) before they can travel.
  • All stakeholders should support and contribute to the rapid sharing of data across the continent.“
 
Statement on new SARS-CoV-2 variant with multiple spike protein mutations – Africa CDC
22 DECEMBER 2020


“Recommendations to Member States and health authorities

Coincidentally, the news of this variant has come when the continent is also experiencing a second wave of the COVID-19 pandemic. Therefore, Africa CDC advises that Member States reinforce their efforts to increase testing, contact tracing and early treatment of cases while we seek to gain more insight about the impact this new variant could have on testing accuracy, clinical outcomes and vaccine efficacy.

Specifically, we recommend that:

  1. Member States increase general awareness of the new variant and take timely measures to monitor, prevent and control its spread.
  2. Public health laboratories and researchers should strengthen collaboration and coordination with national and regional pathogen genomics laboratories in order to conduct genomic surveillance and sequencing of the virus in a timely manner. The Africa CDC IPG, through the Africa Pathogen Genomics Initiative, will support this coordination at the continental level.
  3. Member States should notify Africa CDC immediately if they identify any new SARS-CoV-2 variant.
  4. Member States should enhance community-based surveillance for early identification of hotspots and continue to encourage community members to adhere to public health and social measures for their protection.
  5. Member States and Africa CDC Regional Collaborating Centres should enhance surveillance and cross-border health measures at ports of entry, but there is no immediate need for restrictions on travel and trade.
Africa CDC will continue to monitor the situation and provide updates to Member States and the public as more information becomes available about this SARS-CoV-2 variant.“
 
Statement on new SARS-CoV-2 variant with multiple spike protein mutations – Africa CDC
22 DECEMBER 2020

Additional resources

Information on the U.K. lineage is available the COVID-10 Genomics UK Consortium Website (https://www.cogconsortium.uk/news/) and on virological.org website (Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations)
 
5 days ago / video discusses future threats of new contagions
 
New coronavirus variant appears to emerge in Nigeria, Africa CDC says
December 24, 2020

““The alert about the apparent new variant was based on two or three genetic sequences, he said, but that and South Africa's alert late last week were enough to prompt an emergency meeting of the Africa CDC this week.

The variant was found in two patient samples collected on Aug. 3 and Oct. 9 in Nigeria's Osun state, according to a working research paper seen by The Associated Press.

Unlike the variant seen in the U.K., "we haven't observed such rapid rise of the lineage in Nigeria and do not have evidence to indicate that the P681H variant is contributing to increased transmission of the virus in Nigeria. However, the relative difference in scale of genomic surveillance in Nigeria vs the U.K. may imply a reduced power to detect such changes," the paper says.”

(adding to notes on variants)
 
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“And on Dec. 24, the head of the Africa Centers for Disease Control and Prevention, John Nkengasong, announced the discovery of yet another variant, this one in Nigeria, called B.1.207.“

*note different name from above post, named in red.
 
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Source

The South Africa variant (501Y.V2)
Where and when was it discovered?
This mutation was found in South Africa in early October and announced in December, when the country’s health minister said the strain seemed to affect young people more than previous strains. This variant may have contributed to a surge of infections and hospitalizations across South Africa.

Where is it?
This mutation has been identified in more than two dozen countries, including Canada, Australia and Israel, but not in the United States.

What makes it different?
This mutation shares some similarities to the U.K. variant and, like that strain, appears to be more transmissible. There is no evidence that it is more lethal. Scott Gottlieb, former director of the Food and Drug Administration, has suggested that this variant might be more resistantto antibody therapies.

Will vaccines work?
The vaccines may have a diminished impact against this variant, but they probably will still be effective, Fauci said in January. Moderna has said its vaccine protects against the South Africa variant, with an important caveat: The vaccine-elicited antibodies were also less effective at neutralizing this mutation in a laboratory dish.

Related
Moderna vaccine protects against British and South African variants, company says

South Africa’s second coronavirus wave is fueled by a new strain, teen ‘rage festivals’
 
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