H5N1

China Covid: Experts estimate 9,000 deaths a day as US says it may sample wastewater from planes

Via The Guardian: China Covid: experts estimate 9,000 deaths a day as US says it may sample wastewater from planes. Excerpt:

The United States is considering sampling wastewater taken from international aircraft to track any emerging new Covid-19 variants as infections surge in China, as UK-based health experts estimate about 9,000 people a days are now dying of the disease in China.  

The proposed of testing wastewater by the US Centers for Disease Control and Prevention would provide a better solution to tracking the virus and slowing its entry into the US than new travel restrictions announced this week, three infectious disease experts said.  

The US and a number of other countries have said travellers from China will require mandatory negative Covid tests.   

Their comments came as UK-based health data firm Airfinity said about 9,000 people in China were probably dying each day from Covid, nearly doubling its estimate from a week ago.

Covid infections started to sweep across China in November, picking up pace this month after Beijing dismantled its zero-Covid policies including regular PCR testing on its population and publication of data on asymptomatic cases.  

Cumulative deaths in China since 1 December likely reached 100,000, with infections totalling 18.6m, Airfinity said in a statement on Thursday. It used modelling based on data from Chinese provinces before the recent changes to reporting cases were implemented, it said.  

Airfinity expects China’s Covid infections to reach their first peak on 13 January with 3.7m cases a day.  

Their figures were in contrast to the several thousands of cases reported by Chinese health authorities a day, after a nationwide network of PCR test sites was largely dismantled and authorities pivoted from preventing infections to treating them.  

The European Union’s health agency said on Thursday it believed the EU-wide introduction of mandatory Covid screenings for travellers from China was currently “unjustified”, pointing to the “higher population immunity in the EU/EEA, as well as the prior emergence and subsequent replacement of variants currently circulating in China”.  

But in a series of tweets, the World Health Organization chief, Tedros Adhanom Ghebreyesus, renewed his appeal to China to be more forthcoming with detailed data on the pandemic situation in the country.  

“In the absence of comprehensive information from China, it is understandable that countries around the world are acting in ways that they believe may protect their populations,” Tedros wrote.

Genomic epidemiology of the first two waves of SARS-CoV-2 in Canada

Via eLife: Genomic epidemiology of the first two waves of SARS-CoV-2 in Canada. The abstract:

Tracking the emergence and spread of SARS-CoV-2 lineages using phylogenetics has proven critical to inform the timing and stringency of COVID-19 public health interventions. We investigated the effectiveness of international travel restrictions at reducing SARS-CoV-2 importations and transmission in Canada in the first two waves of 2020 and early 2021. 

Maximum likelihood phylogenetic trees were used to infer viruses’ geographic origins, enabling identification of 2263 (95% confidence interval: 2159–2366) introductions, including 680 (658–703) Canadian sublineages, which are international introductions resulting in sampled Canadian descendants, and 1582 (1501–1663) singletons, introductions with no sampled descendants. 

Of the sublineages seeded during the first wave, 49% (46–52%) originated from the USA and were primarily introduced into Quebec (39%) and Ontario (36%), while in the second wave, the USA was still the predominant source (43%), alongside a larger contribution from India (16%) and the UK (7%). 

Following implementation of restrictions on the entry of foreign nationals on 21 March 2020, importations declined from 58.5 (50.4–66.5) sublineages per week to 10.3-fold (8.3–15.0) lower within 4 weeks. Despite the drastic reduction in viral importations following travel restrictions, newly seeded sublineages in summer and fall 2020 contributed to the persistence of COVID-19 cases in the second wave, highlighting the importance of sustained interventions to reduce transmission. Importations rebounded further in November, bringing newly emergent variants of concern (VOCs). 

By the end of February 2021, there had been an estimated 30 (19–41) B.1.1.7 sublineages imported into Canada, which increasingly displaced previously circulating sublineages by the end of the second wave. Although viral importations are nearly inevitable when global prevalence is high, with fewer importations there are fewer opportunities for novel variants to spark outbreaks or outcompete previously circulating lineages.

See also this CTV report on the study.

Emergence in southern France of a new SARS-CoV-2 variant of probably Cameroonian origin harbouring both substitutions N501Y and E484K in the spike protein

Via medRxiv: Emergence in Southern France of a new SARS-CoV-2 variant of probably Cameroonian origin harbouring both substitutions N501Y and E484K in the spike protein. This preprint first appeared on December 24. The abstract:

SARS-CoV-2 variants have become a major virological, epidemiological and clinical concern, particularly with regard to the risk of escape from vaccine-induced immunity. Here we describe the emergence of a new variant. 

For twelve SARS-CoV-positive patients living in the same geographical area of southeastern France, qPCR testing that screen for variant-associated mutations showed an atypical combination. The index case returned from a travel in Cameroon. The genomes were obtained by next-generation sequencing with Oxford Nanopore Technologies on GridION instruments within approximately 8 h. Their analysis revealed 46 mutations and 37 deletions resulting in 30 amino acid substitutions and 12 deletions. Fourteen amino acid substitutions, including N501Y and E484K, and 9 deletions are located in the spike protein. 

This genotype pattern led to create a new Pangolin lineage named B.1.640.2, which is a phylogenetic sister group to the old B.1.640 lineage renamed B.1.640.1. Both lineages differ by 25 nucleotide substitutions and 33 deletions. The mutation set and phylogenetic position of the genomes obtained here indicate based on our previous definition a new variant we named 'IHU'. 

These data are another example of the unpredictability of the emergence of SARS-CoV-2 variants, and of their introduction in a given geographical area from abroad.

ECDC epidemiological update: Omicron variant of concern (VOC) – data as of 6 December 2021 (12.00)

ECDC has published Epidemiological update: Omicron variant of concern (VOC) – data as of 6 December 2021 (12.00).

As of 6 December and since 5 December 2021, 30 additional SARS-CoV-2 Omicron variant of concern (VOC) cases have been confirmed in the European Union and European Economic Area (EU/EEA), contributing to an overall total of 212 confirmed cases to date. Cases have been reported by 18 countries: Austria (11), Belgium (9), Czechia (1), Denmark (32), Finland (7), France (25), Germany (15), Greece (1), Iceland (12), Ireland (1), Italy (9), Latvia (2), the Netherlands (18), Norway (19), Portugal (34), Romania (2), Spain (7), and Sweden (7) according to information from public sources.  

One new EU/EEA country (Latvia) has reported the Omicron variant, and a number of probable cases are currently under investigation in several countries.  

Based on publicly available and restricted sources, the majority of confirmed cases have an epidemiological link to cases with a history of travel to African countries, with some of those having taken connecting flights at other locations between Africa and Europe. Several EU/EEA countries (Belgium, Denmark, Germany, Spain) detected cases without an epidemiological link to areas where community transmission of the Omicron variant is documented or presumed. This indicates that undetected community transmission could be ongoing in these countries. Finland reported cases with travel history within the EU/EEA (Sweden).  

All cases for which there is available information on severity were either asymptomatic or mild. No deaths have been reported among these cases so far. These figures should be assessed with caution as the number of confirmed cases is too low to understand if the disease clinical spectrum of Omicron differs from that of previously detected variants.  

Countries and territories outside of the EU/EEA have reported 693 confirmed cases. The 29 countries reporting confirmed cases are: Argentina, Australia, Botswana, Brazil, Canada, Chile, Hong Kong Special Administrative Region, Ghana, India, Israel, Japan, Malaysia, Maldives, Mexico, Nepal, Nigeria, Saudi Arabia, Senegal, Singapore, South Africa, South Korea, Sri Lanka, Switzerland, Tunisia, the United Arab Emirates, the United States of America, the United Kingdom, Zambia and Zimbabwe. Overall, globally there have been 905 confirmed cases reported by 47 countries.

ECDC epidemiological update: Omicron variant of concern (VOC) – data as of 5 December 2021 (12.00)

ECDC has published Epidemiological update: Omicron variant of concern (VOC) – data as of 5 December 2021 (12.00).

As of 5 December and since 4 December 2021, 16 additional SARS-CoV-2 Omicron variant of concern (VOC) cases have been confirmed in the European Union and European Economic Area (EU/EEA), contributing to an overall total of 182 confirmed cases to date.  

Cases have been reported by 17 countries: Austria (11), Belgium (9), Czechia (1), Denmark (18), Finland (7), France (16), Germany (15), Greece (1), Iceland (7), Ireland (1), Italy (9), the Netherlands (18), Norway (19), Portugal (34), Romania (2), Spain (7) and Sweden (7) according to information from public sources. One new EU/EEA country (Romania) has reported the Omicron variant and a number of probable cases are currently under investigation in several countries.  

The majority of confirmed cases have a history of travel to countries in Africa, with some having taken connecting flights at other locations between Africa and Europe. Several EU/EEA countries (Belgium, Germany, Spain) detected cases without an epidemiological link to areas where community transmission of the Omicron variant is documented or presumed. This indicates that undetected community transmission could be ongoing in these countries. Finland reported cases with travel history within the EU/EEA (Sweden).  

All cases for which there is available information on severity were either asymptomatic or mild. No deaths have been reported among these cases so far. These figures should be assessed with caution as the number of confirmed cases is too low to understand if the disease clinical spectrum of Omicron differs from that of previously detected variants.  

Correction: Luxembourg’s case (source: GISAID open database) in yesterday’s epi update is pending official country confirmation.

ECDC epidemiological update: Omicron variant of concern (VOC) – data as of 4 December 2021 (12.00)

ECDC has published Epidemiological update: Omicron variant of concern (VOC) – data as of 4 December 2021 (12.00). Click though to download the full report.

As of 4 December and since 3 December 2021, 58 additional SARS-CoV-2 Omicron variant of concern (VOC) cases have been confirmed in the European Union and European Economic Area (EU/EEA), contributing to an overall total of 167 confirmed cases so far.     

Cases have been reported by 17 countries: Austria (10), Belgium (6), Czechia (1), Denmark (18), Finland (1), France (12, including 2 in Reunion), Germany (15), Greece (1), Iceland (7), Ireland (1), Italy (9), Luxembourg (1), the Netherlands (18), Norway (19), Portugal (34), Spain (7) and Sweden (7) according to information from public sources. One new EU/EEA country (Luxembourg) has reported the Omicron variant and a number of probable cases are currently under investigation in several countries.    

The majority of confirmed cases have a history of travel to countries in Africa, with some having taken connecting flights at other locations between Africa and Europe. Several EU/EEA countries (Belgium, Germany, Spain) detected cases without an epidemiological link to areas where community transmission of the Omicron variant is documented or presumed. This indicates that undetected community transmission could be ongoing in these countries. Finland reported cases with travel history within the EU/EEA (Sweden, Denmark).    

All cases for which there is available information on severity were either asymptomatic or mild. No deaths have been reported among these cases so far. These figures should be assessed with caution as the number of confirmed cases is too low to understand if the disease clinical spectrum of Omicron differs from that of previously detected variants.   

ECDC epidemiological update: Omicron variant of concern (VOC) – data as of 2 December 2021 (12.00)

ECDC has published Epidemiological update: Omicron variant of concern (VOC) – data as of 2 December 2021 (12.00). Click through for more.

As of 2 December 2021, and since 1 December 2021, 20 additional SARS-CoV-2 Omicron VOC cases have been confirmed, bringing the total to 79 confirmed cases. The cases have been reported by 15 European Union and European Economic Area (EU/EEA) countries: Austria (4), Belgium (3), Czechia (1), Denmark (6), France (2, including 1 in Réunion), Germany (10), Greece (1), Iceland (1), Ireland (1), Italy (9), the Netherlands (16), Norway (4), Portugal (14), Spain (3), and Sweden (4), according to information from public sources. Four new EU/EEA countries reporting Omicron variant cases are: Iceland, Ireland, Greece, and Norway.  

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. Several European countries reported cases without a travel history who also had no known contact with a case with a travel history (Belgium, Germany, and the United Kingdom).  

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 16 countries and territories outside of the EU/EEA (Australia, Botswana, Brazil, Canada, Hong Kong Special Administrative Region, Ghana, Israel, Japan, Nigeria, Saudi Arabia, South Africa, South Korea, Switzerland, United Arab Emirates, United States of America, and the United Kingdom). Overall, 390 confirmed cases have been reported in 31 countries.

ECDC epidemiological update: Omicron variant of concern (VOC) – data as of 1 December 2021 (12.00)

ECDC has published Epidemiological update: Omicron variant of concern (VOC) – data as of 1 December 2021 (12.00). Click through to download the full report.

As of 1 December 2021, and since 30 November 2021, 15 additional SARS-CoV-2 Omicron VOC cases have been confirmed, bringing the total to 59 confirmed cases. The cases have been reported by 11 European Union and European Economic Area (EU/EEA) countries: Austria (3), Belgium (2), Czechia (1), Denmark (4), France (1, in Réunion), Germany (9), Italy (4), the Netherlands (16), Portugal (14), Spain (2), and Sweden (3), according to information from public sources.  

A number of probable cases have also been reported from across the region, but are still under investigation. The majority of confirmed cases have a history of travel to southern 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. To date, there have been no severe cases and no deaths reported among these cases.  

Cases have been reported in 12 countries and territories outside the EU/EEA (Australia, Botswana, Brazil, Canada, Hong Kong Special Administrative Region, Israel, Japan, Nigeria, Saudi Arabia, 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.