H5N1

ECDC epidemiological update: Omicron variant of concern (VOC) – data as of 30 November 2021 (12.00)

ECDC has published Epidemiological update: Omicron variant of concern (VOC) – data as of 30 November 2021 (12.00).

As of 30 November 2021, 44 confirmed cases of SARS-CoV-2 Omicron VOC have been reported by eleven European Union and European Economic Area (EU/EEA) countries (Austria, Belgium, Czechia, Denmark, France (Reunion), Germany, Italy, the Netherlands, Portugal, Spain and Sweden) according to information from public sources.  

A number of probable cases have also been reported from across the region, but these are still under investigation. The majority of confirmed cases have a history of travel to African countries, with some having taken connecting flights at other destinations between Africa and Europe. All cases for which there is information available  on severity were either asymptomatic or had mild symptoms. So far, no severe cases or deaths have been reported among these cases.  

Cases have been reported in nine countries and territories outside of the EU/EEA (Australia, Botswana, Canada, Hong Kong Special Administrative Region, Israel, Japan, South Africa, Switzerland and the United Kingdom).

ECDC: Epidemiological update: Omicron variant of concern (VOC) – data as of 29 November 2021 (12:30)

ECDC has published Epidemiological update: Omicron variant of concern (VOC) – data as of 29 November 2021 (12:30).

As of 29 November 2021, 33 confirmed SARS-CoV-2 Omicron VOC cases have been reported by eight European Union and European Economic Area (EU/EEA) countries (Austria, Belgium, Czechia, Denmark, Germany, Italy, Netherlands, Portugal) according to information from public sources.  

A number of probable cases have also been reported from across the region, but these are still under investigation. All confirmed cases have a history of travel to African countries, with some having taken connecting flights at other destinations between Africa and Europe. All cases for which there is available information on severity were either asymptomatic or mild. No severe cases and no deaths have been reported among these cases so far.  

Cases have been reported in seven countries and territories outside of the EU/EEA (Australia, Botswana, Canada, Hong Kong Special Administrative Region, Israel, South Africa, United Kingdom).

Minister De Jonge: '13 Omicron infections on Schiphol flights'

Via De Telegraaf: Minister De Jonge: ’13 Omicron infections on Schiphol flights'. The Google translation:

THE HAGUE - During the explanation of Health Minister Hugo de Jonge, it was announced that at least 13 people among the Dutch passengers from South Africa were infected with the omicron variant. No additional measures against this corona variant were announced on Sunday.

Of the more than 600 passengers who arrived in two planes from Cape Town and Johannesburg at Schiphol, it was previously found that 61 had tested positive for corona. The new virus variant has been identified in thirteen of them, the RIVM reports.

The infected passengers are currently staying in a corona hotel near Schiphol Airport. People with complaints must stay there for seven days. Security is available.  

Corona test street Schiphol  

Travelers who have returned from southern Africa since last Monday are urged by De Jonge to be tested and to go into quarantine. From Sunday they can make an appointment via the special number 0800-5005.  

People returning from South Africa via Schiphol can also have themselves tested for the corona virus at the airport from Sunday immediately after arrival. The GGD Kennemerland has set up a special test street at the airport for this purpose. 

These are travelers from South Africa, Namibia, Botswana, Zimbabwe, Mozambique, Malawi, Lesotho and Eswatini (Swaziland). These countries now have an entry ban for non-EU citizens. The Dutch can still travel back and forth to southern Africa. Upon return to the Netherlands, they must have a double negative test result and must be in home isolation for at least five days on arrival. According to De Jonge, the municipality is coming to check whether they are actually staying at home.

Belgium was the first European country where the variant was established, followed on Saturday by England and Germany. The World Health Organization (WHO) has given the variant the stamp of concern, but as yet it is unclear what the consequences are for the severity of the disease and the effectiveness of vaccines.

Growing list of nations on alert over variant

Via The New York Times: Omicron Updates and Covid News: Growing List of Nations on Alert Over Variant. For some reason, the nations declaring travel bans on southern Africa are not imposing such bans on one another. Excerpt:

Dutch health officials said on Sunday they had found at least 13 cases of the Omicron coronavirus variant among 61 infected passengers who had arrived in the Netherlands from South Africa on Friday. The new cases were a clear sign that the virus was crossing borders even as governments imposed new travel restrictions and flight bans.  

Additional cases could emerge, as health officials were still examining test samples, said Hugo de Jonge, the country’s health minister, adding that the people who tested positive were in quarantine. The 61 passengers who had tested positive were among more than 500 who arrived on two separate flights.  

A growing list of countries are scrambling to respond to the new, highly mutated version of the virus, which was first detected in Botswana and South Africa and which has sent ripples of panic through governments and markets. Health officials in Australia and Denmark on Sunday both confirmed cases of the Omicron variant in travelers recently arriving from southern Africa.  

The World Health Organization warned on Friday that Omicron was a “variant of concern,” the most serious category the agency uses for such tracking, and said that its numerous genetic mutations could help it spread more quickly, even among vaccinated people.  

Scientists cautioned that relatively little is known about the new variant, and that only a small number of confirmed cases have surfaced globally. Still, there are worries that Omicron could have spread more widely before scientists in South Africa discovered it last week, and the memories of the rampaging spread this year of the Delta variant have prompted new waves of travel restrictions, aimed primarily at southern African countries.

Britain, Italy, Belgium, the Netherlands and Israel are among the countries that have identified Omicron infections in recent days and imposed new travel restrictions. In a sign of how seriously the authorities in Europe, which is already battling a surge of coronavirus cases, are taking the new threat, officials in France on Friday also suspended arrivals from seven southern African countries even though the new variant had not yet been detected in France.  

“It’s probably a question of hours, let’s be honest,” Olivier Véran, the health minister, told reporters on Sunday at a vaccination center in Paris. But he added that “new variant doesn’t necessarily mean new wave, or that the variant is more dangerous.” 

“To be safe, we are acting as though this variant is potentially dangerous,” he said.

CHP provides latest information on COVID-19's Variant of Concern, Omicron

Via the Centre for Health Protection: CHP provides latest information on COVID-19's Variant of Concern, Omicron.

The Centre for Health Protection (CHP) of the Department of Health (DH) today (November 27) said that since it announced on November 25 two confirmed cases carried viruses which belonged to a newly emerged lineage, B.1.1.529, the CHP has been closely monitoring and following up the latest development of the mutant strain concerned.  

In view of the latest announcement by the World Health Organization (WHO) concerning the Omicron variant, the Government implemented last night (November 26) the most stringent boarding and quarantine requirements for eight places in southern Africa. 

Starting tomorrow (November 28), the CHP will further strengthen the quarantine and testing requirements for Hong Kong Special Administrative Region (HKSAR) residents arriving from the relevant places, including arranging them to stay in quarantine centre for seven days. 

The WHO has designated B.1.1.529 as a Variant of Concern and named it Omicron on November 26 (Geneva time). The mutant strain possesses a large number of mutations and it was first reported to the WHO from South Africa on November 24. In addition, according to the European Centre for Disease Prevention and Control, this mutant strain is the most divergent variant during the COVID-19 pandemic so far. This raises concerns that it may be associated with increased transmissibility, reduction in vaccine effectiveness and increased risk for reinfections.

According to official sources, apart from the information on mutant strain involving two cases provided by the HKSAR Government, the Omicron variant has been detected in a number of places including Botswana, South Africa, Israel and Belgium. To facilitate further risk assessment, the CHP has contacted the health authorities of Israel and Belgium for details about the imported cases there.

Locally, according to the whole genome sequencing conducted by the DH's Public Health Laboratory Services Branch, there are so far two cases which had been announced earlier (cases 12388 and 12404) detected to be carrying the Omicron variant. The CHP has earlier arranged for persons who had stayed from November 11 to 14 in the three rooms to the left and to the right of the two rooms concerned (Rooms 5111 and 5112) of Regal Airport Hotel to undergo compulsory quarantine at the Penny's Bay Quarantine Centre for 14 days. No new related case was detected so far.

The Government has been closely monitoring the latest scientific data on mutant strains as well as the epidemic situation of various places and will adjust the boarding, quarantine and testing requirements for persons arriving at Hong Kong from relevant places based on the risk levels as the situation warrants. 

In view of the latest developments of the Omicron variant, started from 0.00am today, along with South Africa which was already a Group A specified place, the Government also specified Botswana, as well as the adjacent Eswatini, Lesotho, Malawi, Mozambique, Namibia and Zimbabwe as Group A specified places. Non-Hong Kong residents who have stayed in these places within 21 days will not be allowed to enter Hong Kong. Details on the relevant boarding and compulsory quarantine requirements for respective specified places can be found at www.coronavirus.gov.hk/eng/inbound-travel.html.             

Under existing requirement, persons who have stayed in high-risk Group A specified places on the day of boarding for/arrival at Hong Kong or during the 21 days before that day can only board flights for Hong Kong if they are HKSAR residents who are fully vaccinated and hold a recognised vaccination record. Upon arrival, they have to undergo compulsory quarantine for 21 days in a designated quarantine hotel and undergo six tests during compulsory quarantine, followed by self-monitoring for the subsequent seven days, and have to undergo compulsory testing in a community testing centre on the 26th day of arrival at Hong Kong.

To enhance the surveillance on the Omicron variant, starting from 0.00am tomorrow, the CHP will require HKSAR residents arriving from the eight places in southern Africa concerned to undergo quarantine at the Penny's Bay Quarantine Centre for seven days, during which they have to undergo testing every day and their health conditions will be monitored by healthcare professionals. Upon completion of the seven-day quarantine at quarantine centre, they will be allowed to finish the rest of the compulsory quarantine requirement at the designated quarantine hotel which they have reserved. They are also required to undergo testing on the 9th, 12th, 16th and 19th day and another compulsory testing in a community testing centre on the 26th day of arrival at Hong Kong.

The Government has also stepped up its surveillance on designated quarantine hotels and will ensure their compliance to the infection control requirements at all times. Persons undergoing quarantine are reminded again that they must keep the windows in the hotel room closed and wear the surgical masks when they open the room door.

The spokesman for the CHP said, "Although there are not any direct passenger flights arriving Hong Kong from the eight places in southern Africa concerned currently, we noticed the presence of the Omicron variant in a number of places globally. We must stay vigilant and implement the most stringent anti-epidemic measures to prevent the mutant strain from entering the local community. We will review the effectiveness of those anti-epidemic measures from time to time."

Omicron in Hong Kong: CHP investigates four additional confirmed cases of COVID-19

A November 26 release from the Centre for Health Protection: CHP investigates four additional confirmed cases of COVID-19. This appears to report on three, and possibly four, imported cases involving the Omicron strain. Excerpt and then another report: 

The Centre for Health Protection (CHP) of the Department of Health (DH) announced that as of 0.00am, November 26, the CHP was investigating four additional confirmed cases of coronavirus disease 2019 (COVID-19), taking the number of cases to 12 422 in Hong Kong so far (comprising 12 421 confirmed cases and one probable case).      

The newly reported cases are imported cases. Three of the cases involved mutant strains while the mutation test result of the remaining case is pending. The patients comprise three males and one female, aged 9 to 43. All of them arrived in Hong Kong from Group B specified places (medium-risk). Two patients tested positive during the "test-and-hold" arrangement upon arrival at the Temporary Specimen Collection Centre (TSCC) at Hong Kong International Airport and the remaining two tested positive during quarantine. Among them, case 12427, being a close contact of case 12424 who tested positive at the TSCC, tested positive at the Penny's Bay Quarantine Centre.

A total of 40 cases have been reported in the past 14 days (November 12 to 25) and all of them are imported cases.

Meanwhile, via the Hong Kong Free Press: 4 imported COVID-19 cases found. Excerpt and then a comment:

The Centre for Health Protection today said it is investigating four additional imported COVID-19 cases, three of which involve the L452R mutant strain while the remaining case's mutation test result is pending.

The new cases involve three males and one female, aged nine to 43. All of them arrived from medium-risk places.

Two of the patients tested positive upon arrival at Hong Kong International Airport while the other two were confirmed infected with the virus during quarantine.

The centre noted that the patient of case number 12424 tested positive at the airport and his close contact, case number 12427, tested positive at the Penny's Bay Quarantine Centre. I don't know about the other two cases, but we will likely learn more over the weekend.

Case 12427 is probably the Canadian reported to have contracted the Omicron strain while in quarantine. 

Threat Assessment Brief: Implications of the emergence and spread of the SARS-CoV-2 B.1.1. 529 variant of concern (Omicron) for the EU/EEA

Via ECDC: Threat Assessment Brief: Implications of the emergence and spread of the SARS-CoV-2 B.1.1. 529 variant of concern (Omicron) for the EU/EEA. Click through to download the complete document. The executive summary:

A SARS-CoV-2 variant belonging to Pango lineage B.1.1.529, with a high number of S-gene mutations compared to the original virus was detected at the beginning of November 2021. On 26 November 2021 the variant was designated a variant of concern (VOC) and assigned the label Omicron by the World Health Organization (WHO).  

Executive summary  

The variant is characterised by 30 changes, three small deletions and one small insertion in the spike protein, of these, 15 are in the receptor binding domain. This variant was first detected in samples collected on 11 November 2021 in Botswana and on 14 November 2021 in South Africa. As of 26 November 2021, travel-related cases have also been detected in Belgium, Hong Kong and Israel. The Omicron variant is the most divergent variant that has been detected in significant numbers during the pandemic so far, which raises concerns that it may be associated with increased transmissibility, significant reduction in vaccine effectiveness and increased risk for reinfections. As of 26 November 2021, ECDC has classified this variant as a variant of concern (VOC) due to concerns regarding immune escape and potentially increased transmissibility compared to the Delta variant. 

Risk assessed  

What is the risk associated with the introduction and possible community spread of the SARS-CoV-2 variant Omicron in the EU/EEA?  

There is considerable uncertainty related to the transmissibility, vaccine effectiveness, risk for reinfections and other properties of the Omicron variant. However, given its immune escape potential and potentially increased transmissibility advantage compared to Delta, we assess the probability of further introduction and community spread in the EU/EEA as HIGH. In a situation where the Delta variant is resurgent in the EU/EEA, the impact of the introduction and possible further spread of Omicron could be VERY HIGH.  In conclusion, the overall level of risk for the EU/EEA associated with the SARS-CoV-2 variant Omicron is assessed as HIGH to VERY HIGH.  

Options for response  

Based on the mutation profile of Omicron, partial immune escape is likely. Due to the uncertainties concerning Omicron immune escape properties, a precautionary approach is important and the timely and urgently reinforced implementation of non-pharmaceutical interventions (NPIs) in the EU/EEA is strongly advised.  

Genomic surveillance remains of utmost importance for early detection of the presence of this variant, to enable the following of epidemiological trends and guide containment measures. At this early stage, avoiding travel to and from the known affected areas, as well as increased testing (with sequencing of confirmed cases), and contact tracing of COVID-19 cases with an epidemiological link to the affected areas is strongly advised.  

Due to the ongoing active circulation of the Delta variant, EU/EEA countries are urged to give utmost priority towards vaccination of individuals initially targeted by COVID-19 vaccination programmes that remain unvaccinated or not yet fully vaccinated. Countries should consider a booster dose for those 40 years of age and over, first targeting the most vulnerable and the elderly and could then consider a booster dose for all adults 18 years and older at least six months after completion of the primary series.

WHO: Classification of Omicron (B.1.1.529): SARS-CoV-2 variant of concern

Via WHO: Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern. Excerpt:

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.

New Covid-19 variant is a concern as cases show a sharp increase in Gauteng

Via The Mail & Guardian: New Covid-19 variant is a concern as cases show a sharp increase in Gauteng. I gather this variant will likely be known as Nu. Excerpt:

A new Covid-19 variant that poses cause for concern in South Africa has been identified,  with the majority of cases recorded in Gauteng.  

While the full significance remains uncertain at this stage, the new variant, with the lineage B.1.1.529, “has a high number of adaptations with a concern for predicted immune evasion and transmissibility”, the director of the KwaZulu-Natal Research and Innovation Sequencing Platform (Krisp), Tulio de Oliveira, told a media briefing on Thursday.   

The National Institute for Communicable Diseases (NICD) said it could confirm 22 positive cases of the variant as of Thursday. The department of health, together with leading scientists, hosted the urgent virtual news conference after reports of the possible new variant emerged.   

Oliveira said there had been quick action following the detection of the variant, and that experts were researching a possible cluster outbreak in Gauteng.   

“What is very clear, recent data from detailed analysis show that in many areas of Gauteng, in the city of Johannesburg, we see in the last two days, this fast increase of infections, with a sustainable increase,” he said.  

Drawing from data analysis, Oliveira said there was evidence of a “very unusual constellation of mutations” in the genomes of the variant, adding however that the full significance was still uncertain. The B.1.1.529 variant, which has also been recorded in neighbouring Botswana and further afield in Hong Kong, has more than 30 mutations.   

Putting this in perspective, Oliveira noted that the Beta variant had three mutations and the Delta two, adding: “This new variant has 10 mutations just at the receptor-binding domain. And despite having over 30 mutations, [it is] very different from other circulating variants that were assigned a variant of interest.”  

Oliveira added that not all mutations had been well characterised, and that vaccines remained the critical tool to protect people against the virus.  

In a statement, acting NICD executive director Professor Adrian Puren said it was not surprising that a new variant had been detected in South Africa.   

“Although the data are limited, our experts are working overtime with all the established surveillance systems to understand the new variant and what the potential implications could be. Developments are occurring at a rapid pace and the public has our assurance that we will keep them up to date,” Puren said.  

Stakeholders are meeting the World Health Organisation technical working group on Friday, and expect to assign a Greek name for the new variant then.   

South Africa has recorded a sharp increase in new Covid-19 infections in the past eight days. Detected cases and the percentage of positive tests is rising quickly, particularly in Gauteng, the North West and Limpopo. 

ECDC statement: Risk of very high COVID-19 burden unless public health measures are applied urgently

Via the European Centre for Disease Prevention and Control: ECDC statement: Risk of very high COVID-19 burden unless public health measures are applied urgently.

Statement by Andrea Ammon, ECDC Director. 

Recent modelling scenarios run by ECDC indicate that the potential burden of disease in the EU/EEA from the Delta variant will be very high in December and January unless public health measures are applied now in combination with continued efforts to increase vaccine uptake in the total population.  

Since the beginning of the year, we have seen a rapid roll-out of vaccination programmes in the EU/EEA that has successfully averted deaths and had reduced hospitalisations and transmission. But there are still sub-populations and age groups in which coverage remains lower than desired, even in countries that have achieved good overall vaccination coverage. There are still too many individuals at risk of severe COVID-19 infection whom we need to protect as soon as possible. We need to urgently focus on closing this immunity gap, offer booster doses to all adults, and reintroduce non-pharmaceutical measures.  

Currently, less than 70 per cent of the overall population in the EU/EEA have been fully vaccinated. This leaves a large vaccination gap that cannot be bridged rapidly and gives ample room for the virus to spread.  

Because vaccines offer high protection against severe outcomes of COVID-19 infection, the forecasts are showing that a large number of new COVID-19 hospital admissions will be unvaccinated individuals, in particular unvaccinated individuals in risk groups. The current overall level of vaccination uptake in the EU/EEA will therefore be insufficient to limit the burden of COVID-19 cases and hospitalisations over the winter months, and countries with lower levels of vaccination are at higher risk.  

Increasing COVID-19 vaccination coverage in all eligible age groups, but particularly the elderly, the vulnerable, and healthcare workers should remain the priority for public health authorities. Europe must close immunity gaps in the adult population and ensure effective and equitable coverage across countries and regions.  

Countries should also consider a booster dose for all adults 18 years and older, with a priority for people above 40 years old. This is to increase protection against infection due to waning immunity which could potentially reduce the transmission in the population and prevent additional hospitalisations and deaths. The booster dose is recommended six months after completing the primary schedule at the earliest.  

Rolling out vaccination programmes takes time and the full effect of vaccines only comes two weeks after vaccination. As there is some evidence of waning vaccines effectiveness over time against infection and transmission, it is also important to maintain or reintroduce non-pharmaceutical interventions.  

Motivating people to follow these measures is even more important as we move towards winter and the festive season when more people will travel and gather indoors.  

I am aware that it requires a significant effort from public health authorities and society at large to achieve this goal. But now is the time to walk the extra mile. We have safe and effective vaccines available and until a larger part of the eligible population is immunised, non-pharmaceutical interventions must continue to remain part of our daily routine.