New C.1.2 variant mutating 41 times a year, twice as fast other known Sars-CoV-2 variants

Scientists first detected C.1.2 in May 2021, finding that it was descended from C.1, which scientists found surprising as C.1 had last been detected in January. The new variant has “mutated substantially” compared to C.1 and is more mutations away from the original virus detected in Wuhan than any other Variant of Concern or Variant of Interest detected so far worldwide.

The study also found that the C.1.2 lineage has a mutation rate of about 41.8 mutations per year, which is nearly twice as fast as the current global mutation rate of the other variants. The scientists stated that this short period of increased evolution was also seen with the Alpha, Beta and Gamma variants, suggesting that a single event, followed by a spike in cases, drove faster mutation rates.

Jerusalem Post report

Medrxiv preprint: The continuous evolution of SARS-CoV-2 in South Africa: a new lineage with rapid accumulation of mutations of concern and global detection

 

Delta attempting to brute-force its way past the human immune system

 

 

 

Photo by Abby Savage on Unsplash

South Africa: Delta variant now dominant, hard lockdown imposed, alcohol banned

President Cyril Ramaphosa of South Africa imposed a hard lockdown which included a ban on the sale of alcohol from Monday.

“All gatherings, whether indoors or outdoors, are prohibited, including cultural, social and religious gatherings. Funerals and cremations will continue to be permitted but attendance may not exceed 50 people and all social distancing and health protocols must be observed,” said Ramaphosa.

“Beaches, parks will remain open, however no gatherings will be permitted at such venues.”

He said a curfew will be in place from 9pm until 4am and all non-essential establishments will need to close by 8pm.

Furthermore, travel in and out of Gauteng is prohibited. “Because of the burden in Gauteng, travel in and out of the province for leisure purposes will be prohibited. This does not include work, business of commercial travel, transit through airports or for the transport of goods.”

TimesLive.co.za report

 

 

Photo by Kyle-Philip Coulson on Unsplash

Uganda goes into total lockdown as #coronavirus infections rise

Ugandan President Yoweri Museveni on Friday tightened restrictions in the country following a worrying rise in Covid-19 infections and deaths.

On a day when the country recorded 42 Covid-related deaths and 1,000 new infections, the Ugandan leader stopped the movement of public and private transport vehicles. Only security, emergency and other essential service providers, including the police, firefighters and the military have been exempted.

The new move tightened restrictions imposed a week ago, when cross-district travel was banned, schools closed and other public gatherings restricted yet the deaths continued to rise.

At the Mulago National Referral Hospital in the capital Kampala, a ‘technical fault’ on Wednesday cut off oxygen supply to Covid-19 patients at the facility, leading to the death of several patients. The new highest death toll would arrive two days later when the country reported 42 deaths, raising the number of those killed by the virus to more than 400.

The East African report

 

Image by Charles Nambasi from Pixabay

 

Preprint: Persistent #coronavirus infection and intra-host evolution in association with advanced HIV infection

“Here we present a case of prolonged infection of greater than 6 months with shedding of high titer SARS-CoV-2 in an individual with advanced HIV and antiretroviral treatment failure. …Through whole genome sequencing at multiple time-points, we demonstrate the early emergence of the E484K substitution associated with escape from neutralizing antibodies, followed by other escape mutations and the N501Y substitution found in most variants of concern.”

Preprint: Persistent SARS-CoV-2 infection and intra-host evolution in association with advanced HIV
infection

 

 

Photo by National Cancer Institute on Unsplash

Angola: Increase in #coronavirus infections, hospitalisations and deaths as 2nd wave peaks

Lubango central hospital in Angola is under pressure due to the growing number of patients, reporting the possible collapse of the system. In the Angolan province of Huíla, local health authorities are concerned with the increase in deaths and cases of Covid-19, especially since the beginning of May. The province recorded 14 deaths in the last seven days, an average of two a day, in addition to an increase in hospitalizations for serious and critical cases at the central hospital in Lubango.

In view of the worsening situation and the fear of collapse in the health system, local health authorities are reiterating calls to the population to redouble preventive measures and announced the opening of four new Covid-19 patient care centers in the municipalities of Chibia , Kuvango, Jamba and Cacula and thus try to stop the wear and tear in the largest hospital in the region.

Voaportugues.com report from Angola

 

Uganda was the first country on the continent to confirm the presence of the B.1.617 variant first identified in India late last year.

This variant has now been reported in Kenya, Morocco, Algeria, South Africa, Botswana, Angola, DR Congo, Nigeria, Uganda, Zambia and Zimbabwe.

BBC.co.uk report

 

Africa: Tanzania/Angola #coronavirus variant carries E484K & H655Y mutations

 

India: The stunning rise of the B.1.617.2 #coronavirus variant

 

 

 

Image by Erik Cleves Kristensen – View of Luanda, Angola, CC BY 2.0, https://commons.wikimedia.org/w/index.php?curid=2048784

Ireland: 24 cases of P.1, 55 cases of B.1.351 and 3 cases of B.1.617 reported

Director of the National Virus Reference Laboratory Dr Cillian de Gascun said that there have been three cases of the recent variant [B.1.617] first identified in India. Dr De Gascun said at least two of them are associated with travel. He said NPHET does not have any data to determine whether the variant is more transmissible or not, but said at this stage people need to remain vigilant and try to contain it locally.  Separately, 24 cases of the P.1 variant, which was first found in Brazil, have so far been confirmed in Ireland, while 55 cases of B.1.351 South African variant have also been confirmed.

RTE.ie report

 

Image by Christian_Birkholz from Pixabay

UK: #coronavirus vaccine breakthrough cases reported with B.1.351 and B.1.1.7 variants

People in the UK have been infected with Covid-19 more than once thanks to catching different variants of the coronavirus. Dr Susan Hopkins, chief medical adviser for NHS Test and Trace, said there had been cases where people had become reinfected by different strains of the coronavirus. “We have seen some people who have had their first dose of vaccine who have had the South African variant and the variant that arose in Kent,” she told BBC’s the Andrew Marr show. “You can see that they’re not as good against the South African variant as they are against our own (variant) B117 at preventing infection and transmission.”

KentLive.new report

 

 

Image by Nico Callens from Pixabay

The South African and Brazilian #coronavirus variants can now infect mice

Here we show that unlike the initial virus, VOCs are able to infect common laboratory mice, replicating to high titers in the lungs. This host range expansion is explained in part by the acquisition of changes at key positions of the receptor binding domain that enable binding to the mouse angiotensin-converting enzyme 2 (ACE2) cellular receptor, although differences between viral lineages suggest that other factors are involved in the capacity of SARS-CoV-2 VOCs to infect mice. This abrogation of the species barrier raises the possibility of wild rodent secondary reservoirs

Full BiorXiv preprint

 

Image by Nature_Blossom from Pixabay

Efficacy of the AstraZeneca #coronavirus vaccine against the B.1.351 South African Variant

Study conclusions:  A two-dose regimen of the ChAdOx1 nCoV-19 [AstraZeneca] vaccine did not show protection against mild-to-moderate Covid-19 due to the B.1.351 [South Africa ] variant.

“Between June 24 and November 9, 2020, we enrolled 2026 HIV-negative adults (median age, 30 years); 1010 and 1011 participants received at least one dose of placebo or vaccine, respectively. Both the pseudovirus and the live-virus neutralization assays showed greater resistance to the B.1.351 variant in serum samples obtained from vaccine recipients than in samples from placebo recipients. In the primary end-point analysis, mild-to-moderate Covid-19 developed in 23 of 717 placebo recipients (3.2%) and in 19 of 750 vaccine recipients (2.5%), for an efficacy of 21.9% (95% confidence interval [CI], −49.9 to 59.8). Among the 42 participants with Covid-19, 39 cases (92.9%) were caused by the B.1.351 variant; vaccine efficacy against this variant, analyzed as a secondary end point, was 10.4% (95% CI, −76.8 to 54.8). The incidence of serious adverse events was balanced between the vaccine and placebo groups.”

Full paper on NEJM

 

Image by MasterTux from Pixabay

Antibody resistance of #coronavirus variants B.1.351 (SA) and B.1.1.7 (UK)

“Findings on B.1.351 [South Africa variant] are more worrisome in that this variant is not only refractory to neutralization by most NTD mAbs but also by multiple individual mAbs to the receptor-binding motif on RBD, largely owing to an E484K mutation. Moreover, B.1.351 is markedly more resistant to neutralization by convalescent plasma (9.4 fold) and vaccinee sera (10.3-12.4 fold). B.1.351 and emergent variants13,14 with similar spike mutations present new challenges for mAb therapy and threaten the protective efficacy of current vaccines.

Full Paper on Nature Magazine

 

Image by fernando zhiminaicela from Pixabay

More than 450 cases of the South African #coronavirus variant 501Y.V2 diagnosed in Israel

Over 450 cases of the South Africa coronavirus variant 501Y.V2 have been diagnosed in Israel so far, and health professionals estimate that dozens more are being infected each day.

The Israeli Health Ministry’s committees on vaccinations and the pandemic said two weeks ago that the B.1.351 or 501Y.V2 variant was spreading beyond control.

Haaretz.com full report

 

Image by Orna Wachman from Pixabay

16 cases of new #coronavirus variant VUI-202102/04, B1.1.318 under investigation in Britain

Sixteen cases of a new variant, VUI-202102/04 (lineage B.1.1.318), have been identified in the UK. The variant has been designated a Variant Under Investigation (VUI) by Public Health England (PHE).

Cases of this variant, understood to have originated in the UK, were first identified on 15 February through genomic horizon scanning. All individuals who tested positive and their contacts have been traced and advised to isolate.

Following assessments, the variant was designated a VUI on 24 February. It contains the E484K mutation, which is also found in 2 existing VUIs present in the UK, but does not feature the N501Y mutation, present in all variants of concern (VOCs).

The addition of this variant as a VUI means there are now a total of 4 VUIs and 4 VOCs currently being tracked in the UK.

Gov.uk variant statement

Daily Mail report

 

Image by Stuart Allen from Pixabay