Preprint: Increased risk of SARS-CoV-2 reinfection associated with emergence of the Omicron variant in South Africa

332 individuals were identified who had three suspected infections. Most of these individuals initially tested positive during the first wave, with suspected reinfections associated with waves two and three. One of these individuals had four suspected infections. Among the individuals who have had more than one reinfection, 47 (14.2%) experienced their third infection in November 2021, which suggests that many third infections are associated with transmission of the Omicron variant.

MedrXiv Preprint: Increased risk of SARS-CoV-2 reinfection associated with emergence of the Omicron variant in South Africa

Omicron at 74% of South African genome sequences in November

 

Sars-CoV-2 – checkmate to the virus in four moves

 

Image by Keli Black from Pixabay

WHO: Global risk related to Omicron assessed as very high

WHO: “The overall global risk related to the new VOC Omicron is assessed as very high.”

“Given mutations that may confer immune escape potential and possibly transmissibility advantage, the likelihood of potential further spread of Omicron at the global level is high. Depending on these characteristics, there could be future surges of COVID‐19, which could have severe consequences, depending on a number of factors including where surges may take place. The overall global risk related to the new VOC Omicron is assessed as very high.”

 

 

 

Coronaheadsup from August 2020:

UK: Is Delta already making way for a fitter variant?

 

Image by bhossfeld from Pixabay

B.1.1.529 named “Omicron” and designated a Variant of Concern by the World Health Organisation

“Based on the evidence presented indicative of a detrimental change in COVID-19 epidemiology, the TAG-VE has advised WHO that this variant should be designated as a Variant of Concern, and the WHO has designated B.1.1.529 as a VOC, named Omicron.”

The Technical Advisory Group on SARS-CoV-2 Virus Evolution (TAG-VE) is an independent group of experts that periodically monitors and evaluates the evolution of SARS-CoV-2 and assesses if specific mutations and combinations of mutations alter the behaviour of the virus. The TAG-VE was convened on 26 November 2021 to assess the SARS-CoV-2 variant: B.1.1.529.

The B.1.1.529 variant was first reported to WHO from South Africa on 24 November 2021. The epidemiological situation in South Africa has been characterized by three distinct peaks in reported cases, the latest of which was predominantly the Delta variant. In recent weeks, infections have increased steeply, coinciding with the detection of B.1.1.529 variant. The first known confirmed B.1.1.529 infection was from a specimen collected on 9 November 2021.

This variant has a large number of mutations, some of which are concerning. Preliminary evidence suggests an increased risk of reinfection with this variant, as compared to other VOCs. The number of cases of this variant appears to be increasing in almost all provinces in South Africa. Current SARS-CoV-2 PCR diagnostics continue to detect this variant. Several labs have indicated that for one widely used PCR test, one of the three target genes is not detected (called S gene dropout or S gene target failure) and this test can therefore be used as marker for this variant, pending sequencing confirmation. Using this approach, this variant has been detected at faster rates than previous surges in infection, suggesting that this variant may have a growth advantage.

There are a number of studies underway and the TAG-VE will continue to evaluate this variant. WHO will communicate new findings with Member States and to the public as needed.

Based on the evidence presented indicative of a detrimental change in COVID-19 epidemiology, the TAG-VE has advised WHO that this variant should be designated as a VOC, and the WHO has designated B.1.1.529 as a VOC, named Omicron.

As such, countries are asked to do the following:

  • enhance surveillance and sequencing efforts to better understand circulating SARS-CoV-2 variants.
  • submit complete genome sequences and associated metadata to a publicly available database, such as GISAID.
  • report initial cases/clusters associated with VOC infection to WHO through the IHR mechanism.
  • where capacity exists and in coordination with the international community, perform field investigations and laboratory assessments to improve understanding of the potential impacts of the VOC on COVID-19 epidemiology, severity, effectiveness of public health and social measures, diagnostic methods, immune responses, antibody neutralization, or other relevant characteristics.

Individuals are reminded to take measures to reduce their risk of COVID-19, including proven public health and social measures such as wearing well-fitting masks, hand hygiene, physical distancing, improving ventilation of indoor spaces, avoiding crowded spaces, and getting vaccinated.

For reference, WHO has working definitions for SARS-CoV-2 Variant of Interest (VOI) and Variant of Concern (VOC).

A SARS-CoV-2 VOI is a SARS-CoV-2 variant:

  • with genetic changes that are predicted or known to affect virus characteristics such as transmissibility, disease severity, immune escape, diagnostic or therapeutic escape; AND
  • that has been identified as causing significant community transmission or multiple COVID-19 clusters, in multiple countries with increasing relative prevalence alongside increasing number of cases over time, or other apparent epidemiological impacts to suggest an emerging risk to global public health. 

A SARS-CoV-2 VOC is a SARS-CoV-2 variant that meets the definition of a VOI (see above) and, through a comparative assessment, has been demonstrated to be associated with one or more of the following changes at a degree of global public health significance:

  • increase in transmissibility or detrimental change in COVID-19 epidemiology; OR
  • increase in virulence or change in clinical disease presentation; OR
  • decrease in effectiveness of public health and social measures or available diagnostics, vaccines, therapeutics

WHO.int press release

 

So what is Plan B if the vaccines fail?

Botswana: 4 Omicron cases detected this week were fully vaccinated

A press release from the Covid-19 taskforce of Botswana, outlining details of the first four cases of Omicron variant B.1.1.529 found in Botswana:

 

Nu variant: first European case of B.1.1.529 found in Belgium via Egypt and Turkey

 

 

Photo by Justice Hubane on Unsplash 

Europe declares Omicron variant B.1.1.529 a Variant of Concern

The ECDC has declared the recently discovered Omicron variant B.1.1.529 as a Variant of Concern in its latest bulletin.

It’s unprecedented for this procedure to happen so quickly. The Omicron variant hadn’t even been named by the WHO when the ECDC listed it as a VOC, underlining the very grave potential for this new virus to overtake Delta as the main variant of concern in Europe in the middle of the existing winter wave.

European Centre for Disease Prevention and Control – variants of concern

 

B.1.1.529 named “Omicron” and designated a Variant of Concern by the World Health Organisation

 

Nu variant: first European case of B.1.1.529 found in Belgium via Egypt and Turkey

South Africa: Omicron variant B.1.1.529 has outcompeted Delta in just two weeks

South Africa held a press conference today to give more information on the new SARS-CoV-2 variant B.1.1.529. There is some very concerning news on the variant’s transmission potential, and news that it has already outcompeted all other variants including Delta in just two weeks 

The variant was named Omicron by the World Health Organisation on Friday 26th November 2021.

Professor Tulio de Oliveira, a director of Covid surveillance in the South African province of KwaZulu-Natal, said that the variant had spread rapidly in South Africa.  In less than two weeks it now dominates all infections following a devastating Delta wave in South Africa. We estimate that 90 per cent of cases in Gauteng (at least 1,000 a day) [are this variant].’

 

South African Press conference held 26th November 2021 on the new variant B.1.1.529:

 

A summary of the new B.1.1.529 variant:

 

B.1.1.529 – the potential impact of the mutations:

 

B.1.1.529 – a profile of the mutations:

 

New variant B.1.1.529 has already become the dominant variant in South Africa:

 

B.1.1.529 genomes detected in Gauteng Province in South Africa:

 

South Africa has already seen a large uptick across the country in S-Gene dropouts associated with the new variant:

 

A summary of what is known about B.1.1.529 so far:

 

 

 

 

B.1.1.529: Sars-Cov-2 variant with extremely high number of Spike mutations

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

 

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