Beta COVID-19 variant 501.V2 thread

[Mary Wilson]

Dec 18th, 2020 | Minister Mkhize Speaks

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.

... 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.”

https://sacoronavirus.co.za/2020/12/18/new-covid-19-variant-identified-in-sa

 

[Okieman]

South Africa identifies new coronavirus strain causing surge in cases

JOHANNESBURG (Reuters) - South Africa has identified a new variant of the coronavirus that is driving a second wave of infections, the health minister said on Friday, days after Britain said it had also found a new variant of the virus boosting cases.

“We have convened this public briefing today 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,” Minister of Health Zweli Mkhize tweeted.

“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.

<snip>

South African health authorities said the new variant seemed to spread faster than the previous iteration, but that it was too early to tell its severity and whether current vaccines would work against it.

“In the UK they have also identified a new variant ... there are quite a few similarities between the two lineages ... there are also a similar number of mutations” said Prof Tulio de Oliviera, a member of government’s genomics consortium in a televised briefing.

https://www.reuters.com/article/us-...s-strain-causing-surge-in-cases-idUSKBN28S2HH

 

[gsgs]

> quite a few similarities between the two lineages ... there are also a similar number of mutations”

I haven't seen sequences or mutations yet, but this is hard to believe that the UK and SA strains have common mutations..
Besides N501Y

KRISP : https://www.krisp.org.za/

data at GISAID, while claiming it were "public"

https://www.krisp.org.za/ngs-sa/ngs...dly_but_believe_that_research_should_be_fair/

 

[sharon sanders]

bump this

 

[Mary Wilson]

December 19, 2020
Dr Emma Hodcroft's current thread:

Dr Emma Hodcroft@firefoxx66

Is the new UK variant the same as the new South African variant (501Y.V2)?

No.

They both share the same mutation in spike: N501Y (N->Y at position 501). However, the 2 variants have arisen separately.

12:14 PM ? Dec 19, 2020?Twitter Web App

Dr Emma Hodcroft

In the tree below, the UK variant is in green at the top.

The SA variant is the one with large yellow circles nearer the bottom.

Though it's a bit hard to see in this tree, they are quite distant genetically: they have many mutations they do not share!

...
UK variant & SA variant both have many other mutations that are being investigated.

https://twitter.com/firefoxx66/statu...59989395861506

 

[Mary Wilson]

Experts checking how COVID-19 variant emerged: Prof Karim

19 December 2020, 9:30 PM

Prof Karim says experts are also checking whether the vaccines that will be available next year will work with the variant of the virus.

...“How much of the virus has to change before we regard it as a change in the strain is something that has to be determined by the WHO. The level of reliability we are seeing now would not constitute a strain change. We are not dealing with strains at this time. We are just dealing with a variant so, if you wanna call it as it’s within the family,” says Karim.

https://www.sabcnews.com/sabcnews/experts-checking-how-covid-19-variant-emerged-prof-karim/

 

[Vibrant62]

South Africa appears to also have a rapidly transmissible strain that has arisen independently of the UK variant.

see. https://www.express.co.uk/news/world/1374779/covid-strain-latest-new-coronavirus-variant-south-africa-young-adults

It is feared the strain may now be immune to certain antibodies triggered at the start of the pandemic.

Commenting on the strain, Dr Eric Feigl-Ding said: "New more worrisome South Africa strain: the new 501.V2 variant has troubling details as it seems to spread faster, has a higher viral load and possibly more severe among young adults."

The health minister, Dr Zweli Mkhize has also stated it is unclear whether any current vaccine may have an effect on 501.V2.
https://www.express.co.uk/news/worl...coronavirus-variant-south-africa-young-adults

https://www.express.co.uk/news/worl...coronavirus-variant-south-africa-young-adults

 

[Vibrant62]

See https://flutrackers.com/forum/forum...ovid-19-variant-identified-in-sa-south-africa

 

[Gert van der Hoek]

Britain, Denmark, the Netherlands, and flights from South Africa to Turkey was halted

Health Minister Fahrettin Koca said, "It has been decided to temporarily stop the flights from England, Denmark, the Netherlands and South Africa to our country." found in the description.
Zafer Fatih Beyaz |20.12.2020

 

[Okieman]

New ‘more transmissible’ coronavirus variant discovered in UK


New variant was brought in by travelers from South Africa.
BY WILLIAM ADKINS
December 23, 2020 5:44 pm

British Health Secretary Matt Hancock announced that a new “highly concerning” variant of the coronavirus has been discovered in two individuals returning from South Africa.

“It is yet more transmissible and it appeared to have mutated further than the new variant that has been discovered here,” Hancock said in Wednesday’s Downing Street news conference.

The government is also asking anybody that has been to South Africa in the past two weeks and their close contacts to quarantine immediately. “These measures are temporary, while we investigate this further new strain, which is currently being analyzed,” he added.

<snip>

https://www.politico.eu/article/new-...-restrictions/

 

[Okieman]

SA SEES ITS HIGHEST EVER DAILY INCREASE OF COVID-19 INFECTIONS


The number of deaths continues to rise at an alarming rate as well with 411 fatalities recorded in the last day.

Gladys Mutele | about 11 hours ago
JOHANNESBURG - South Africa has reported a record increase in coronavirus cases with 14,046 new cases detected in the past 24-hours.

This brings the total number of infections in the country to 954,258 since the start of the outbreak in March.

On Wednesday, the health ministry said it was concerned as this indicated that the virus continued to spread exponentially.

Health Minister Zweli Mkhize said the rate of the spread was much faster than the first wave, whose peak would be surpassed in the coming days.

<snip>

This pushes the national COVID-19 related death toll to 25,657 with the most deaths recorded in the Western Cape, followed by Eastern Cape and KwaZulu-Natal.

<snip>

https://ewn.co.za/2020/12/24/sa-sees-its-highest-ever-daily-increase-of-covid-19-infections

(Okieman comment: I am pretty sure that the Western Cape, Eastern Cape and KwaZulu-Natal are the areas in South Africa where the new variant of Covid-19 has been found to be the most widespread.)

 

[Okieman]

WC HOSPITALS SEEING ABOUT 570 ADMISSIONS PER DAY AS COVID PEAK NEARS


South Africa has reported a staggering 14,046 in new confirmed cases in the last 24-hours alone.

Thando Kubheka & Kaylynn Palm | about 6 hours ago
CAPE TOWN/JOHANNESBURG - The Western Cape Health Department is frantically trying to provide more beds for COVID-19 patients as the new variant of the virus tears through the nation like wildfire.

The province currently has the highest number of active cases and authorities say they're seeing around 570 hospital admissions across private and public facilities every single day.

The province suggested earlier this week that the peak would likely hit in the first week of January but that could change.

Western Cape Health's Sadiq Karrim said the rate of increase of new infections was alarming.

“Cases are still exponentially increasing and that’s why we’re trying to quickly bring online additional beds into the service platform. It’s hard to say at the moment when that peak is going to be, whether it’s early or mid-January, but at the moment we’re till noting a very exponential rise in our cases and hospitalisations.”

<snip>

https://ewn.co.za/2020/12/24/wc-hospitals-seeing-about-570-admissions-per-day-as-covid-peak-nears

 

[Okieman]

COVID-19 in SA: Western Cape could ask for military help
Wednesday 23 December 2020 - 5:21am

CAPE TOWN - Western Cape health authorities are looking to the South African military for help, amid the second wave of COVID-19 infections.

Hospitals across the province are under severe strain with health workers pleading for some form of reprieve.

​

Coronavirus cases among health workers continue to spike, while their families, too, are being infected.

Private hospitals are also under pressure with patients being diverted to state hospitals and vice versa.

https://www.enca.com/news/covid-19-sa-western-cape-could-ask-military-help

(Okieman comment: There is also a video worth watching. It is the mention of a spike in health care workers which caught my eye.)

 

[Mary Wilson]

Another new coronavirus variant found in Nigeria, says Africa CDC

DECEMBER 24, 20207:56 AM UPDATED 5 HOURS AGO
By Reuters Staff

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.

https://www.reuters.com/article/us-...ound-in-nigeria-says-africa-cdc-idUSKBN28Y1B7

 

[sharon sanders]

Covid-19: Looking for glimmers of hope in second wave – SA health policy expert Prof Whiteside

24th December 2020 by Melani Nathan

South Africa is in the vice grip of a second wave of the Covid-19 virus. After a year of social isolation, financial pressure, emotional turmoil and fear Covid-19 is delivering an even more devastating blow. A new strain of Sars CoV-2 has been identified. It spreads more easily and younger, healthy people are succumbing to the disease in hospitals, Discovery Health’s Covid-19 expert Dr Ronald Whelan recently told BizNews.com. This second wave is being driven by the new variant and healthcare experts are expressing concern that the latest wave has a much steeper curve with more deaths and intensive care unit admissions. The Western Cape‘s healthcare system is buckling under the wave and private facilities are sending patients into the public sector.

more..

https://www.biznews.com/thought-lead...pe-second-wave

 

[sharon sanders]

Mkhize criticises travel bans, saying there is 'no evidence' new SA variant is more dangerous


Matthew SavidesNight news editor

24 December 2020 - 22:40

Health minister Dr Zweli Mkhize.
Image: theo jeptha

Health minister Dr Zweli Mkhize on Thursday moved to allay fears that the fast-spreading newly-identified Covid-19 variant circulating in SA was more dangerous than variants in other countries.

In a statement on Christmas Eve, Mkhize said that there was "no evidence" of this.

And, said Mkhize, the decision to ban international travel from South Africa was not in line with current scientific evidence.

more..

https://www.timeslive.co.za/news/so...no-evidence-new-sa-variant-is-more-dangerous/

 

[sharon sanders]

Dr Zweli Mkhize

@DrZweliMkhize
?
Dec 23
Today we report, with concern, a cumulative total of 954 258 cases of #COVID19, with 14 046 new cases identified since the last report at a positivity rate of 26%.



458
1.8K

 

[Okieman]

South African health workers stretched as COVID-19 infections near 1 million

By Shafiek Tassiem, Wendell Roelf

JOHANNESBURG/CAPE TOWN (Reuters) - Matron Annamarie Odendaal has cancelled all staff holiday on the COVID-19 ward at the private Arwyp Medical Centre in Johannesburg as a second wave of the coronavirus threatens to overwhelm South Africa’s health system.

<snip>

Private hospital group Mediclinic said the number of patients seeking care at its hospitals in Western Cape and rising incidents in KwaZulu Natal and Gauteng had already exceeded those in the first peak and the majority of its ICU and high care units were operating at full capacity.

“With the new strain we saw that the patients are not recovering so easy and this is a problem,” said matron Odendaal.

During the first wave earlier this year, her hospital had fewer ICU patients, but now “they do not respond well under treatment so they do end up in ICU 90% of the times.”

https://www.reuters.com/article/us-health-coronavirus-safrica-idUSKBN28Z0R0

(I bolded and put in red the last two sentences of this article. I consider this important information.)

 

[Okieman]

'It would appear new Covid-19 variant has higher transmissibility': experts
Claire Keeton

SA's new coronavirus variant has rapidly displaced others but little is known about it yet - including whether it makes people sicker - though preliminary data suggests it is highly transmissible.

Known as 501Y.V2, it has quickly become the main variant circulating in Western Cape and Eastern Cape hotspots. Carolyn Williamson, head of medical virology at the University of Cape Town, said samples from the Garden Route in October contained no virus mutations. By early November, about 40% showed the V2 mutation and by late November it was up to 80%.

"There are 20 different variants but this one has rapidly dominated," Williamson said.

Willem Hanekom, director of the Africa Health Research Institute in KwaZulu-Natal and head of a research consortium of 33 scientists investigating the new variant, said it was the dominant lineage of the second wave.

The variant emerged in the Eastern Cape and spread rapidly to the Western Cape. It has not yet been identified conclusively in Gauteng or the Free State, according to the scientists who are analysing it.

Hanekom said: "It is likely to [reach] everywhere if it follows the patterns. It is likely to transmit more easily and we have heard reports that younger people are more infected and [sicker] with it than any other variants. We need to confirm this."

<snip>

https://www.timeslive.co.za/sunday-...-variant-has-higher-transmissibility-experts/

 

[Okieman]

‘New wave’ Covid-19 curbs loom as hospitals fill up, oxygen is rationed

27 December 2020 - 00:05BY CLAIRE KEETON

Tougher restrictions could be imposed nationwide when the National Coronavirus Command Council meets this week to discuss a Covid-19 resurgence, partly driven by a highly transmissible mutation of the virus.

<snip>

Dr Andrea Mendelsohn, a senior Western Cape medical officer, wrote in an open letter to Cape Town this week: "Once the beds are full and oxygen used up - we are rapidly approaching that point - then my hospital and so many others will not be able to help. They will be clearing stations for corpses. This is my nightmare and yours.

"If hypoxic patients - where there's a lack of oxygen in the blood - are put on a waiting list for high-flow nasal oxygen, they are in all likelihood waiting to die, she wrote, appealing to people to wear masks, practise social distancing and socialise outdoors.

Dr Katrin St?ve, a senior internal medicine specialist at Helderberg Hospital in Somerset West, said people were "a lot sicker this time, with patients between 30 and 50, with no comorbidities, more critical and succumbing to the disease". She added: "In our hospital we have a small oxygen tank that used to be filled once a week, but now it gets filled every day."

<snip>

https://www.timeslive.co.za/sunday-...loom-as-hospitals-fill-up-oxygen-is-rationed/

(Okieman Comment: I suggest taking the time to read this article. I have bolded and put in red some of the text I found to be most important. It is one that is hard to read but I believe the world needs to look at this variant very closely. Most of the media is giving lots of attention to the UK variant, and understandably so, but this variant may be significantly more dangerous.)