Category: South Africa
Preprint: Omicron incompletely escapes immunity induced by the Pfizer vaccine
Laboratory research from South Africa strongly suggests that the SARS-CoV-2 Omicron variant escapes antibody immunity induced by the Pfizer-BioNTech (Comirnaty) vaccine, but that considerable immunity is retained in people who were both vaccinated and previously infected.
“The clinical implications of these important laboratory data need to be determined. It is likely that lesser vaccine-induced protection against infection and disease would be the result. Importantly, most vaccinologists agree that the current vaccines will still protect against severe disease and death in the face of Omicron infection. It is therefore critical that everyone should be vaccinated,” said Africa Health Research Institute executive director Professor Willem Hanekom.
The research has been submitted to medRxiv. To access an advance copy of the manuscript, click here.
Image by Thomas Anderson from Pixabay
South Africa: Omicron BA.1 and BA.2 – “One has an S-gene dropout, the other not”
Well that escalated quickly…
Omicron, BA.1, and BA.2 – We need to follow them closely. One has an S-gene drop out the other not. Genomics surveillance and qPCR are essential to control it as it spreads widelyl.
— Tulio de Oliveira (@Tuliodna) December 7, 2021
Tulio de Oliveira is Director of CERI: Centre for Epidemic Response & innovation, South Africa
Delta attempting to brute-force its way past the human immune system
Preprint: Omicron is the product of extensive evolution that has left no obvious traces of intermediate forms
The Omicron variant identified in Southern Africa in late November 2021 is the product of extensive evolution within an infection context that has so far left no obvious traces of intermediate forms since it diverged from the B.1.1 lineage (presumably at some time in mid to late 2020).
“Our analysis identifies three clustered sets of mutations in the Spike protein, involving 13 amino acids that have previously been highly conserved across SARS-CoV-2 and other Sarbecoviruses. This dramatic about-face in evolutionary dynamics at these 13 sites suggests that Omicron’s Spike protein structure has accommodated significant sequence change, likely in response to selective pressures favoring increased transmission,immune evasion, or viral replication—either at the population level or in a single or group of chronically infected individuals—and has potentially acquired new functionality.”
Preprint: Selection analysis identifies significant mutational changes in Omicron that are likely to influence both antibody neutralization and Spike function
South Africa: Tshwane District Omicron Patient Profile
There has been a significant rise in new SARS-CoV-2 infections in the Gauteng Province in the last four weeks which has been attributed to the new Omicron variant announced on 24 November 2021. The first cases of Omicron were detected in the Tshwane District and coincided with the sharp rise in new infections, heralding the onset of the fourth wave in Gauteng.
Tshwane has been the global epicentre of the Omicron Outbreak and the Gauteng Province Fourth Wave with the weekly number of cases rising exponentially over several weeks, reaching just over 8569 cases in Epi Week 47 (21 November -November 27 and 41 921 by 3 December before the end of Epi Week 48 (28 November to 4 December). The exponential rise in cases has continued with 9929 new cases reported in Tshwane in the last 5 days from 29 November to 3 December 2021 (Figure 1).
We report on the early experience of the patient profile at the Steve Biko/Tshwane District Hospital Complex in Pretoria, in the heart of the Tshwane District.
Image by Jean van der Meulen from Pixabay
South Africa: Growing number of children admitted to hospitals with Omicron
South African health care workers are raising concern about the growing number of children being hospitalised with moderate to severe symptoms of the Omicron variant of the coronavirus.
Head of Intensive Care at Chris Hani Baragwanath hospital, Dr Rudo Mathivha says the situation is worrying because the hospital isn’t built to admit a high number of sick young children.
She says a 15-year-old died after the child’s condition deteriorated rapidly following a COVID-19 infection, and a 17-year-old is in ICU with coronavirus-related pneumonia.
Update: 4th December 2021
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
Image by Keli Black from Pixabay
Omicron at 74% of South African genome sequences in November
Stunning figures showing the explosive growth of the new Omicron variant in South Africa. The latest genome sequences are showing 74% Omicron variant for November.
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:
Omicron “incubated in an immunocompromized person for months or serially passaged in a lab”
Some interesting developments on the possible origins of the new Omicron variant, B.1.1.529…
The @nextstrain https://t.co/wVE7ubYBoy focal build for 21K (B.1.1.529) is now live.https://t.co/UD1WPcJphP
As previously, the long branch leading to 21K is clearly visible, making it hard with current sequences to tell much about the evolutionary history. https://t.co/dQSPFv2lwm pic.twitter.com/hoxllKKTho
— Dr Emma Hodcroft (@firefoxx66) November 26, 2021
Looks like the new strain was either incubated in an immunocompromized person for months or serially passaged in a lab in the presence of convalescent plasma — along the lines of what the Italians did a while back. https://t.co/h8AyMcVJBH
— Yuri Deigin (@ydeigin) November 27, 2021
https://nextstrain.org/groups/neherlab/ncov/21K
Netherlands: “Dozens” infected with Covid on flights from South Africa
Dutch health authorities said that dozens of people who arrived in Amsterdam on two flights from South Africa on Friday are likely infected with COVID-19, and they are conducting further testing to see if people are infected with the recently discovered Omicron coronavirus variant.
Around 600 passengers arrived at Amsterdam’s Schiphol Airport on the two KLM flights on Friday and then faced hours of delays and testing due to concerns over the new virus variant.
** The latest figure we have seen is 61 people are infected from the two planes.
Image by Lars_Nissen from Pixabay
Israel: four potential Omicron cases flew in from Malawi, Jordan
The South African Omicron variant was first discovered in Israel late Thursday night, according to reports released Friday morning by the Health Ministry. It was first detected in an individual who returned to Israel from Malawi. Two other cases of returnees from abroad were also later identified as suspicious.
In all three cases, the travellers were vaccinated. According to media reports, one traveller was inoculated with three doses of the Pfizer vaccine, one with two shots of AstraZeneca and the other with two shots of Johnson & Johnson.
Later, another individual who entered Israel from Jordan was also found suspicious of infection with the variant.
More…
Hundreds of passengers from South Africa were being held at Schiphol Airport in Amsterdam on Friday after the Netherlands imposed new travel restrictions amid concerns over an aggressive mutation of the Covid-19 virus.
Two flights from South Africa, one from Cape Town and one from Johannesburg, landed Friday late morning local time at Schiphol, an airport spokesman said. The passengers had to remain on board the flight while a separate, secure location in the airport was being located and are waiting to be tested, he said.
Omicron variant: first European case of B.1.1.529 found in Belgium via Egypt and Turkey
Image by Tobias Rehbein 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
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
Omicron variant: first European case of B.1.1.529 found in Belgium via Egypt and Turkey
A woman with coronavirus symptoms after a trip to Egypt with a stopover in Turkey is the first confirmed case in Belgium of a patient infected with the new variant B.1.1.529, known as ‘Omicron’, initially located by the scientific community in the Southern African countries. She also becomes the first patient in Europe to be infected with the ‘Omicron’ variant.
The diagnosis has been confirmed by the UZ Leuven University Hospital (Leuven) after examining a young adult who was not vaccinated and who began to develop symptoms eleven days after having made the trip to Egypt, according to the Belgian chain RTBF.
This is the first confirmed case in Europe of this variant that is related to southern African countries, although the patient, who has a high viral load, does not seem to have any recent link with that region, according to the information provided by the case.
The diagnosis coincides with a proposal by the European Commission to close the border common to flights with origin or destination in the southern African region, a measure that the 27 have yet to examine on the afternoon of this Friday.
Before the case of the young woman infected in Belgium was revealed, precisely the Belgian Minister of Health, Frank Vandenbroucke, indicated in a press conference that he fully adheres to the proposal to restrict flights to the region for the sake of “prudence“, despite the fact that “not much is known yet” about the variant.
El Periodico report (in Spanish)
Image by Iwo Bulski from Pixabay