India: 16% vaccine breakthrough in Delhi hospital #coronavirus study

A small-scale study on 113 healthcare workers who had received at least one vaccine dose at a private hospital in Delhi found that 18 tested positive for Covid but all except one had mild symptoms.  Of the 113 in the study, 107 had received the second dose of the vaccine.

Taken in percentage form, the study found that breakthrough infections — Covid infection in vaccinated individuals — occurred in 15.9 per cent (18 persons) of the vaccinated individuals and 95 per cent had mild symptoms. Of these, 17 incurred the infection after the second dose. According to the study, of the breakthrough infections in 18 persons, 17 incurred the infection after the second dose. These 17 had got their second dose after a mean of 34.8 days following the first jab.

NDTV report

Belgium: Five fully vaccinated care home residents infected with B.1.617.3 in vaccine breakthrough outbreak

Seychelles: 30% #coronavirus vaccine breakthrough rate

Image by shalender kumar from Pixabay

WHO: B.1.617 Indian #coronavirus strain is now a Variant of Concern or VOC

A World Health Organization official said Monday it is reclassifying the Indian Sars-Cov-2 variant B.1.617 as a “variant of concern,” indicating that it’s become a global health threat. Maria Van Kerkhove, the WHO’s technical lead for Covid-19, said the agency will provide more details in its weekly situation report on the pandemic Tuesday but added that the variant, known as B.1.617, has been found in preliminary studies to spread more easily than the original virus and there is some evidence it may able to evade vaccines.

“as such we are classifying this as a variant of concern at the global level,” she said during a press conference. “Even though there is increased transmissibility demonstrated by some preliminary studies, we need much more information about this virus variant in this lineage in all of the sub lineages, so we need more sequencing, targeted sequencing to be done.”

 

Belgium: Five fully vaccinated care home residents infected with B.1.617.3 in vaccine breakthrough outbreak

Five residents of a care home in Borsbeek in Antwerp province have been infected with the so-called Indian variants of Covid-19, according to the Flemish Agency for Health and Care. One of those affected has died.  All of the home’s residents have been fully vaccinated.

In three of the cases involved in the new outbreak, the Indian variant has been confirmed, and it is supposed the same goes for the other two. One has since died, and another is in hospital.

Brussels Times report

 

Image by meineresterampe from Pixabay

India: B1617 twice as infectious as UK #coronavirus variant B117

Early indications from an analysis of the growth of the B.1.617 variant of the Covid-19 virus has shown it to be at least twice as infectious as the UK variant and thrice as infectious as the variant behind last year’s Covid-19 wave.

Scientists involved in the whole genome sequencing as part of the Centre’s Covid-19 genomic surveillance exercise told The New Indian Express that this conclusion is based on the growth of this mutant, as compared to others, in districts where B.1.617 has been identified along with other variants in samples collected from infected individuals.

“We have been examining this data carefully and the way this lineage of virus, also called the double mutant, is growing as compared to others is remarkable,” said a senior scientist involved in the INSACOG project, a consortium of several institutions under the National Centre for Disease Control that carry out an extensive genomic surveillance. “For the public, what needs to be communicated very clearly is that there is a greater need to double mask and maintain social distancing as this virus is highly infectious.

New Indian Express report

** Update **  Tom Wenseleers: “Based on this data, the new variant from India has a very big transmission or growth advantage,” even over B.1.1.7, he says. “It’s kind of like the U.K. variant squared.”

 

UK: Indian #coronavirus variant B.1.617.2 already outcompeting B.1.1.7 in some areas of Britain

 

India: The stunning rise of the B.1.617.2 #coronavirus variant

 

UK government poised to declare Indian #coronavirus B.1.617 a Variant of Concern or VOC

 

 

Image by Free-Photos from Pixabay

UK: Indian #coronavirus variant B.1.617.2 already outcompeting B.1.1.7 in some areas of Britain

UK GOV: “B.1.617.2 has spread rapidly in India based on available data. There have been multiple importations to the UK and onwards transmission within the UK. In some regions, S gene target data suggests that this variant may be more frequent than is indicated by the current sequence data, due to the lag in sequencing, and may have replaced B.1.1.7 to some extent. Modelled growth estimates suggest that the variant is at least as transmissible as B.1.1.7. Further analyses are required with targeted comparator groups and improved correction for importation to refine the position on transmissibility. Some early laboratory data suggest limited antigenic change. There are insufficient data as yet to assess reinfection or vaccine effectiveness through national surveillance.”

UK.GOV: SARS-CoV-2 variants of concern and variants under investigation in England, Technical briefing 10 (PDF download)

 

India: The stunning rise of the B.1.617.2 #coronavirus variant

 

UK: India is added to travel “red list” three weeks too late

 

Image by Free-Photos from Pixabay

UK: surge testing for Indian #coronavirus VOC B.1.617.2 begins in Bolton as some areas see 500% increase in cases

Mobile Covid-19 testing units are being rolled out in Bolton as surge testing gets underway in the borough’s coronavirus hotspots. People in Rumworth, Deane or Great Lever are being urged to get tested at the units. Infection rates in those areas have increased, ­ with Rumworth South seeing cases rocket by 500 per cent, with an infection rate of 359.3 per 100,000 people. In Lever Edge, part of Great Lever, cases have increased by 40 per cent.

Bolton currently has the second highest infection rate in the UK.

The Bolton News Report

 

UK: B.1.617 found in 24% of #coronavirus sequences in Bolton, mostly new VOC B.1.617.2

 

India: The stunning rise of the B.1.617.2 #coronavirus variant

 

Image by David Reed from Pixabay

France: 40 cases of Breton variant B.1.616 (20C/655Y) with #coronavirus mutations D614G, H655Y, G669S & V482A

As of April 28, 40 cases of infection with the 20C/655Y (B.1.616) variant have been confirmed (37 in Brittany, three in other regions). The diagnosis was made on a first positive RT-PCR from a sample nasopharyngeal in 13% of them, and from a deep sample in 68% of cases. All cases have a direct or indirect link with the enhanced surveillance zone in Brittany. The majority of cases are linked to transmissions within hospital clusters in the area. A few cases have been reported in link with a chain of transmission in the community but, to date, the monitoring indicators do not suggest a significant community diffusion of this variant in the population, whether in Brittany or elsewhere. Epidemiological investigations are continuing to characterize the episode and monitor the diffusion of this variant.

French Health Department Document: COVID-19: epidemiological update of April 29, 2021 (PDF download)

 

France: Breton variant B.1.616 – 37 cases & 16 deaths with just 9% of cases detected by first RT-PCR #coronavirus test

France: 32 cases of Breton #coronavirus variant B.1.616 reported

 

Image by françois zimmermann from Pixabay

UK: B.1.617 found in 24% of #coronavirus sequences in Bolton, mostly new VOC B.1.617.2

Following a rise in cases in the UK and evidence of community transmission, PHE has reclassified B.1.617.2 as a Variant of Concern (VOC). This is based on evidence which suggests this variant, first detected in India, is at least as transmissible as B.1.1.7 (the Kent variant). The other characteristics of this variant are still being investigated.

Cases of B.1.617.2 have increased to 520 from 202 over the last week and almost half the cases are related to travel or contact with a traveller. The cases are spread across the country, however, the majority of the cases are in 2 areas – the North West (predominantly Bolton) and London – and this is where we are seeing the greatest transmission.

PHE Document – Confirmed cases of COVID-19 variants identified in UK

 

India: The stunning rise of the B.1.617.2 #coronavirus variant

 

UK government poised to declare Indian #coronavirus B.1.617 a Variant of Concern or VOC

 

India: double mutant coronavirus variant B.1.617 outcompeting B.1.1.7 UK variant

 

Image by David Mark from Pixabay

UK government poised to declare Indian #coronavirus B.1.617 a Variant of Concern or VOC

The UK government is thought to have detected more than 40 clusters of the Indian Covid variant B.1.617 in the UK, and is on the verge of declaring it a “variant of concern”. The mutant strain is thought to be driving the massive surge of infections in India.

Channel 4 News report

India: The stunning rise of the B.1.617.2 #coronavirus variant

India: double mutant coronavirus variant B.1.617 outcompeting B.1.1.7 UK variant

 

Image by Adam Derewecki from Pixabay

India: The stunning rise of the B.1.617.2 #coronavirus variant

Professor Christina Pagel:  [B.1.617] rapidly became dominant in India and, again the sequenced data there is sparse, but early modelling shows that it might well be more transmissible than our B.117 Kent strain. ‘What we have also seen in India is that B.1.617.2 is becoming the dominant subtype – exactly the same pattern we see here in the UK.  ‘While this could reflect the situation in India through importation, the Sanger data tries to exclude travel related cases or surge testing and we still see the rise of B.1.617.2 in that’.

 

WHO: B.1.617 Indian #coronavirus strain is now a Variant of Concern or VOC

UK government poised to declare Indian #coronavirus B.1.617 a Variant of Concern or VOC

 

** NOTE: B.1.617.2 carries the T478K mutation according to the European Centre for Disease Prevention and Control

See also Bioxriv preprint: Preliminary report on SARS-CoV-2 Spike mutation T478K

 

Rapid rise of #coronavirus SARS-CoV-2 spike mutation T478K found in Mexico and several European countries

 

Chart courtesy of Outbreak.info

 

NEJM “a recombination event between B.1.1.7 and B.1.526” #coronavirus variants

Examination of the SARS-CoV-2 sequences revealed that both patients were infected with variant viruses. Rapid identification of sequence variants by targeted PCR amplification showed that neither sequence precisely fit any known clade. Some of the substitutions in Patient 1 (T95I, del144, E484K, A570D, D614G, P681H, and D796H) were shared with B.1.526 (T95I, E484K, and D614G6), and three substitutions were shared with Patient 2 (in whom the variants T95I, G142V and del144, F220I, R190T, R237K, R246T, and D614G were detected). Whole viral genome sequencing revealed several additional substitutions, including D796H, present in a guanine–cytosine–rich region not identified by targeted PCR. These substitutions may decrease sensitivity to convalescent serum11 and may have some unique noncoding changes as compared with the clades first identified in Wuhan, the United Kingdom, and New York City.

Although more detailed analysis of whole-genome sequencing from Patient 1 was undertaken, we could not conclude that the variant in this patient was a Pango lineage because it was only present in a single person.

Its closest links on the phylogenetic tree were the variant first identified in the United Kingdom (B.1.1.7) and the variant first identified in New York City (B.1.526), but with considerable differences. It will be of interest to determine whether this may have resulted from a recombination event between B.1.1.7 and B.1.526, as has been recently reported for recombination between the B.1.1.7 lineage and the “wild-type” lineage first identified in Wuhan. Alternatively, shared substitutions may be the result of convergent evolution.

NEJM: Vaccine Breakthrough Infections with SARS-CoV-2 Variants

 

See also:

NEJM: In two #coronavirus vaccine breakthrough cases “examination of the SARS-CoV-2 sequences revealed that both patients were infected with variant viruses” .. “neither sequence precisely fit any known clade”

NEJM: In two #coronavirus vaccine breakthrough cases “examination of the SARS-CoV-2 sequences revealed that both patients were infected with variant viruses” .. “neither sequence precisely fit any known clade”

Examination of the SARS-CoV-2 sequences revealed that both patients were infected with variant viruses. Rapid identification of sequence variants by targeted PCR amplification showed that neither sequence precisely fit any known clade. Some of the substitutions in Patient 1 (T95I, del144, E484K, A570D, D614G, P681H, and D796H) were shared with B.1.526 (T95I, E484K, and D614G6), and three substitutions were shared with Patient 2 (in whom the variants T95I, G142V and del144, F220I, R190T, R237K, R246T, and D614G were detected).

NEJM article  “Vaccine Breakthrough Infections with SARS-CoV-2 Variants”

 

Image by Daniel Roberts from Pixabay

Severe Acute Respiratory Syndrome #Coronavirus 2 (SARS-CoV-2) in a Dog, Connecticut, February 2021

Here, we report the first natural infection case of SARS-CoV-2 in dogs in Connecticut. On February 12, 2021, a 3-months-old, female German Shepard dog was presented for postmortem examination at Connecticut Veterinary Medical Diagnostic Laboratory due to sudden death with no signs of illness, as reported by the owner.

“We report the first detection of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus from a dog in Connecticut during February 2021. Complete genome sequencing and phylo-genetic analysis of the hCoV-19/USA/CT-CVMDL-Dog-1/2021 (CT_Dog/2021) virus were con-ducted to identify the origin and lineage of the virus. The CT_Dog/2021 virus belonged to the GH/B1.2. genetic lineage and was genetically close to SARS-CoV-2 identified from humans in the U.S. during the winter of 2020-2021. However, it was not related to other SARS-CoV-2 identified from companion animals in the U.S. It contained both D614G in spike and P323L in nsp12 substitutions which have become the dominant mutations in the United States. The continued sporadic detections of SARS-CoV-2 in companion animals warrant public health concerns about their potential to become a new reservoir species of SARS-CoV-2.”

Preprints.org link