Category: Genome
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
Norway: 42 infected in SECOND Christmas dinner superspreader event – Omicron suspected
42 people have so far been diagnosed with Covid following a Christmas dinner at Maarud on Saturday 27th November. It includes company employees, hosts, entertainment actors and a few household members for people who attended the Christmas table.
Supposedly every third person present during the event has been diagnosed with corona. About half of the infected people live in South Odal.
The municipality mayor thinks there is reason to believe that in this outbreak of infection there is a talk about the omikron variant, but the municipality has not yet received answers to the tests sent to Ahus for sequencing.
VG.no report (in Norwegian)
Update 7th December 2021: Approaching 60 corona-infected after the Maarud Christmas table
The infection rate after the Christmas table at the potato gold producer Maarud last Saturday is now approaching 60.
The municipality of Sør-Odal in the Inland, where the Christmas table was held, stated on Tuesday that ten new inhabitants have been diagnosed with the coronavirus in the last 24 hours.
Norway: Nearly 100 Omicron infections from one Oslo Christmas party
Photo by Simon Williams on Unsplash
Belgium: Two hippos test positive for Sars-Cov-2 in Antwerp Zoo
Two hippos have tested positive for Covid-19 at Antwerp zoo, according to a press release.
“Both animals, Imani and Hermien, apart from a runny nose, show no other symptoms and are doing well,” the ZOO says. “The animals are in isolation and the keepers are taking even stricter safety measures.”
The cause of the infection is not known. ZOO Antwerp says none of the keepers have recently contracted the disease, nor have any staff members shown any symptoms.
** A list of all animals infected with Sars-Cov-2 that we have reported on over the last two years can be found here under our “Animals” category
Image by Kiều Trường from Pixabay
UKHSA risk assessment for Omicron variant
UK risk assessment for Omicron variant B.1.1.529, dated 3rd December 2021
Transmissibility between humans: Amber – At least as transmissible as currently circulating variants
Omicron is transmitting rapidly and successfully. Increased transmissibility compared to Delta is
biologically plausible with the presence of furin cleavage site and nucleocapsid changes
associated in vitro with advantages for replication, as well as extensive changes to the RBD.
Structural modelling suggests that the mutations present may increase human ACE2 binding
affinity to a much greater extent than that seen for any other variant.
Phylogeny suggests a recent emergence. Data from South Africa suggests that Omicron has a
pronounced growth advantage there. However, this may be due to transmissibility or immune
escape related, or both.
Naturally acquired immunity: Red – Mutations suggestive of reduced protection from natural immunity and limited supporting epidemiological evidence
Based on experience with other variants, laboratory data on individual mutations, and structural
modelling, the mutations present are very likely to reduce antibody binding and include changes
in all 4 neutralising antibody binding sites in the RBD and also in antigenic sites in the S NTD. T
cell epitope data is awaited. Analysis from South Africa suggests a reduction in protection from
previous infection, including from recent Delta infection. There is no convalescent sera
neutralisation data and no relative risk of reinfection analyses as yet.
Vaccine-derived immunity: Red – Mutations suggestive of reduced protection from vaccine derived immunity, no supporting evidence
The mutations present are likely to reduce antibody binding and include changes in all 4 RBD
neutralising antibody binding sites. T cell epitope data is awaited. There is no vaccinee sera
neutralisation data and no epidemiological data on vaccine effectiveness.
Therapeutics: Red – Mutations suggestive of reduced effectiveness of a treatment in UK clinical use
The mutations present are likely to reduce the binding of most available therapeutic monoclonal
antibodies, based on structural modelling. On the same basis, they are unlikely to affect current
small molecule antivirals. However, there is no laboratory or clinical data to support these
predictions at present.
Norway: Nearly 100 Omicron infections from one Oslo Christmas party
Another 20-30 people have been registered infected with Covid after a Christmas dinner at a restaurant in Oslo at the end of November. This is in addition to the 60 who have already been registered infected.
The infected people visited the restaurant Louise Restaurant & Bar at Aker Brygge in Frogner, Oslo, at the same time as a Christmas table was held at the restaurant. They are thus in addition to the around 60 Christmas table participants who have already been registered infected, reports NRK.
Dagsavisen.no report (in Norwegian)
Note: The number of people infected with the Omicron variant from this one Christmas party could now be nearly 100. The original guest list was said to be about 120 people, although some of the new infections reported today are related to other patrons who were at the same venue on the same day. All of the guests invited to the Christmas party were fully vaccinated and were asked to take a Covid test before attending.
Norway: Omicron superspreader event sees about 60 fully vaccinated people infected
Image by Alexandra von Gutthenbach-Lindau from Pixabay
Norway: 37,000 people tested for Covid following tractor fair outbreak
37,000 Norwegians have been asked to test themselves following a Covid infection outbreak at a trade fair. Several people who visited a tractor fair in Lillestrøm, Norway last week have tested positive for Covid-19.
It is still unclear whether those infected at the fair were infected with the new Omicron variant of the coronavirus. The Omicron variant has appeared in several parts of Norway and led the authorities to tighten their pandemic measures.
SVT.se report (in Swedish)
Update: The tractor fair location in Lillestrøm is less than 30km from Frogner, in Oslo, where another superspreader event involving 60 Omicron infections took place around the same time.
Israeli doctor believes he caught Omicron variant of Covid in London
Cardiologist Elad Maor suspects he caught virus at conference attended by more than 1,200 people.
The doctor who is one of the first people in the world to become infected with the Omicron variant says he believes he caught the virus when he was in London for a major medical conference attended by more than 1,200 health professionals.
The disclosure from Elad Maor will raise fears that the variant may have been in the UK much earlier than previously realised – and that other medics could have been exposed to it too.
Israel: Triple jabbed doctor found infected with Omicron after flight from London
UK: Third Omicron case confirmed, was last seen in Westminster
Israel: Triple jabbed doctor found infected with Omicron after flight from London
Two Israeli cardiologists have been confirmed as infected with the Omicron variant, a spokesperson for Sheba hospital confirmed. Both doctors were fully vaccinated with three shots of the Pfizer coronavirus vaccine.
One of the doctors, in his 50s, brought the variant into Israel on return from a medical conference in London. He tested negative when he boarded the airplane from the United Kingdom to Israel and on arrival, but a few days later began experiencing symptoms.
Israeli doctor believes he caught Omicron variant of Covid in London
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:
FT: dozens of suspected Omicron cases in the UK
“A third Omicron case was identified in the UK and dozens more were being treated as suspected cases, people familiar with the matter told the Financial Times.”
UK: Third Omicron case confirmed, was last seen in Westminster
Image by Gordon Johnson from Pixabay
UKHSA risk assessment for Sars-CoV-2 variant AY.4.2
AY.4.2 continues to increase in prevalence slowly in England. There is an increased growth rate for AY.4.2 compared to other circulating variants in 2 separate models, and this is now consistent across regions of England.
There is a small increase in secondary attack rate and in household transmission risk, though both these analyses have limitations as they are derived from routine testing and tracing data systems.
There is also a slowly increasing prevalence and an increased growth rate for AY.4.2 in incoming travellers to the UK. However, there is as yet no other country reporting the same effect through domestic surveillance and there is some conflicting evidence from community survey data. Confidence in this finding therefore remains low.
UKHSA Risk assessment for Sars-CoV-2 variant AY.4.2
Preprint: Genome recombination between Delta and Alpha variants of SARS-CoV-2
Prominent genomic recombination has been observed between the Delta and Alpha variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolated from clinical specimens in Japan.
During the surveillance, we monitored several variants of concern (VOCs) of the PANGO lineage. We found six unique specimens among the 21A (Delta) clade isolates that exhibited a low quality assignment (“not determined” or “none”) in the PANGO lineage, even though their genome sequences had been completely determined with high read coverage throughout the whole genome region.
A detailed genome alignment by Nextclade suggested that despite being clonal isolates of the 21A (Delta) clade, these six isolates show identical mutation profiles with 20I (Alpha, V1), particularly between the ORF6 and N genes, located towards the latter part of the SARS-CoV-2 genome.
Additionally, the alignment clearly revealed a possible recombination spot between the ORF6 and ORF7a genes. However, the next generation sequencing (NGS)-based read mapping analysis did not indicate the presence of any heterogeneous mix of alleles in the clinical specimens, suggesting that these patients had not acquired multiple variant infections with 21A (Delta) and 20I (Alpha, V1) clades at the acute stage of the infection.
MedRxiv preprint: Genome Recombination between Delta and Alpha Variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)
Image by Iván Tamás from Pixabay
Israel: Hospital acquired infections despite full PPE, N-95 mask, face shield, gown and gloves
We have investigated a nosocomial COVID-19 outbreak involving the SARS-CoV-2 Delta variant among a highly vaccinated population. The attack rate among exposed individuals reached 23.3% in patients and 10.3% in staff, with 96.2% vaccination rate among exposed individuals. Moreover, several transmissions probably occurred between two individuals both wearing surgical masks, and in one instance using full PPE, including N-95 mask, face shield, gown and gloves.
Although reports of breakthrough infections are increasing, this communication emphasises several points. It challenges the assumption that high universal vaccination rates will lead to herd immunity and prevent COVID-19 outbreaks. This was probably true for the wild-type SARS-CoV-2 virus, but in the outbreak described here, 96.2% of the exposed population was vaccinated. Infection advanced rapidly (many cases became symptomatic within 2 days of exposure), and viral load was high.
Eurosurveillance.org report: Nosocomial outbreak caused by the SARS-CoV-2 Delta variant in a highly vaccinated population, Israel, July 2021
Japan: Delta sub-lineage AY.29 found in 88% of samples
In the present study, we report a new sub-lineage of the SARS-CoV-2 Delta variant called AY.29, which has C5239T and T5514C mutations. We investigated the monthly trend of AY.29 in Japan within 11,954 Delta variants downloaded on September 3, 2021. Among the total Japanese Delta variants, the AY.29 sub-lineage accounted for 88.4%. In terms of monthly changes, the sequences became predominant in June, and accounted for 93.2% and 94.2% of the reported sequences in July and August, respectively.
Preprint: Genomic Surveillance in Japan of AY.29 – A New Sub-lineage of SARS-CoV-2 Delta Variant with C5239T and T5514C Mutations
Image by abdulla binmassam from Pixabay