UK: learning to live with COVID-19 cannot mean simply allowing infections to spread unchecked causing hospitalisations, illness – including Long COVID, and deaths

Joint Statement from the Association of Directors of Public Health and the Faculty of Public Health on the COVID-19 Roadmap.

Whilst the Roadmap is coming to an end on the 19th July, COVID-19 is not.

Learning to live with COVID-19 cannot mean simply allowing infections to spread unchecked causing hospitalisations, illness – including Long COVID, and deaths; and increasing the possibility of new variants of concern. Evidence shows carefully selected public health messages and measures both limit transmission and provide the foundation for a sustainable economic and social recovery, rather than being a roadblock.

ADPH and FPH continue to argue for a combination approach to protecting our communities. The vaccination rollout is a huge success and allows us to move closer to normality, but it is far from complete. Therefore, handwashing, ventilation, testing, isolating and face coverings in high-risk settings remain vital tools.

Balanced measures, clear communication and the collective effort of everyone are key to easing restrictions and keeping cases at low levels. This is a challenging moment and caution is crucial.

Joint Statement from the Association of Directors of Public Health and the Faculty of Public Health on the COVID-19 Roadmap.

 

 

Image by Cor Gaasbeek from Pixabay

From Alpha to Delta – how Britain won and then lost the fight against coronavirus

After months of being ravaged by the Alpha variant (B.1.1.7) in 2020, Britain seemed to turn a corner in its fight with the coronavirus in early 2021. After a gruelling lockdown, the Alpha variant was fading fast, and, by the middle of May 2021, Britain was within touching distance of Zero Covid. Then, through lax border controls, Delta was allowed to enter the country, and the infection cycle restarted.

Will Britain make the same mistake with the *next* variant of concern? With borders opening and “Freedom Day” on the horizon, it’s a racing certainty.

Images courtesy of UK.gov

UK: PHE data shows B.1.617.2 now outcompetes B.1.1.7

More amazing work by Prof. Christina Pagel in deciphering the latest Public Health England data dumps for B16172. It’s well worth reading the whole thread!  The UK’s laissez faire attitude to border control and quarantine enforcement means that, after B.1.1.7, Britain is, once again, about to export a highly dangerous Sars-Cov-2 VOC worldwide. 

 

 

 

UK: #coronavirus variant B.1.617.2 within hours of outcompeting B.1.1.7 in Britain

WHO: Newly designated VOC within lineage B.1.617 – update on Delta #coronavirus variant

In consultation with the WHO SARS-CoV-2 Virus Evolution Working Group, WHO has determined that viruses within the lineage B.1.617 have been characterized as a VOC. B.1.617 contains three sub-lineages, which differ by few but potentially relevant mutations in the spike protein as well as prevalence of detection globally.

As of 11 May, over 4500 sequences have been uploaded to GISAID and assigned to B.1.617 from 44 countries in all six WHO regions, and WHO has received reports of detections from five additional countries. Though there may be important differences among the three sublineages, currently available evidence is too limited for VOI/VOC characterization by sublineage.

Future delineation of sublineages as VOIs/VOCs may be possible as our understanding by sublineage and relative importance of their epidemiology increases. At the present time, WHO has designated B.1.617 as a VOC based on early evidence of phenotypic impacts compared to other circulating virus variants, namely:

  • B.1.617 sublineages appear to have higher rates of transmission, including observed rapid increases in prevalence in multiple countries (moderate evidence available for B.1.617.1 and B.1.617.2), and
  • Preliminary evidence suggests potential reduced effectiveness of Bamlanivimab, a monoclonal antibody used for COVID-19 treatment, and potentially slightly reduced susceptibility to neutralisation antibodies (limited evidence available for B.1.617.1).

Viruses in the B.1.617 lineage were first reported in India in October 2020. The resurgence in COVID-19 cases and deaths in India has raised questions on the potential role of B.1.617 and other variants (e.g., B.1.1.7) in circulation. A recent risk assessment of the situation in India conducted by WHO found that resurgence and acceleration of COVID-19 transmission in India had several potential contributing factors, including increase in the proportion of cases of SARS-CoV-2 variants with potentially increased transmissibility; several religious and political mass gathering events which increased social mixing; and, under use of and reduced adherence to public health and social measures (PHSM). The exact contributions of these each of these factors on increased transmission in India are not well understood.

Approximately 0.1% of positive samples in India have been sequenced and uploaded to GISAID to identify SARS-CoV-2 variants. The prevalence of several VOCs including B.1.1.7 and B.1.612 sublineages increased concurrent to the surge in COVID-19 cases reported in India. While B.1.1.7 and B.1.612.1 variants have begun to wane in recent weeks, a marked increase in the proportion of viruses sequenced as B.1.612.2 has been observed over the same period. Since the identification of these variants through late April 2021, B.1.617.1 and B.1.617.2 accounted for 21% and 7% of sequenced samples from India, respectively.

A preliminary analyses conducted by WHO using sequences submitted to GISAID suggests that B.1.617.1 and B.1.617.2 have a substantially higher growth rate than other circulating variants in India, suggesting potential increased transmissibility compared. Too few sequences of B.1.617.3 have been detected to date to assess its relative transmissibility. Other studies suggest that the case numbers increased more rapidly during the most recent surge when variants B.1.1.7 and B.1.617 were circulating, compared to the first surge (June to October 2020).

A structural analysis of B.1.617 receptor binding domain (RBD) mutations (L452R and E484Q, along with P681R in the furin cleavage site) suggest that mutations in these variants may result in increased ACE2 binding and rate of S1-S2 cleavage resulting in better transmissibility, and possibly capacity to escape binding and neutralization by some monoclonal antibodies.

In a preliminary study on hamsters, infection with B.1.617.1 resulted in increased body weight loss, higher viral load in lungs and pronounced lung lesions as compared to B.1 variants (D614G).

Potential impacts of B.1.617 lineage on effectiveness of vaccines or therapeutics, or reinfection risks, remain uncertain. Preliminary laboratory studies awaiting peer review suggest a limited reduction in neutralisation by antibodies; however, real-world impacts may be limited. e One study found a seven-fold reduction in neutralization effectiveness against B.1.617.1 of antibodies generated by vaccination with Moderna – mRNA-1273 and Pfizer BioNTech-Comirnaty vaccines.

A second study also found a reduction in neutralization against virus carrying the E484Q mutation (contained in B.1.617.1 and B.1.617.3) for Pfizer BioNTech – Comirnaty vaccine, similar to that found with the E484K mutation.

A third study reviewing a limited sample of convalescent sera of COVID-19 cases (n=17) and sera from recipients of the Bharat – Covaxin vaccine (n=23) concluded that most neutralizing activity against B.1.617 was retained.

A fourth study reported an approximately three-fold decrease in neutralization activity by plasma from recipients of Pfizer BioNTech – Comirnaty vaccine (n=15) against B.1.617, and a limited two-fold decrease by convalescent sera from cases with severe COVID-19 (n=15). The same study showed that B.1.617.1 (with additional spike mutations R21T, and Q218H) mediates increased entry into certain human and intestinal cell lines, and was resistant to the monoclonal antibody Bamlanivimab; however, it was efficiently inhibited by Imdevimab and by a cocktail of Casirivimab and Imdevimab.

Outside of India, the United Kingdom has reported the largest number of cases sequenced as B.1.617 sub-lineages, and recently designated B.1.617.2 as a national variant of concern. This follows a recent steep increase in the number of cases sequenced as B.1.617 sublineages, and a national assessment that characterized B.1.617.2 as at least equivalent in terms of transmissibility as VOC B.1.1.7; however, they noted insufficient data to assess the potential for immune escape.

As of 5 May, the United Kingdom has reported 520 genomically confirmed B.1.617.2 cases (of which approximately two-thirds were domestically acquired), 261 confirmed B.1.617 cases (without further delineation), and nine confirmed B.1.617.3 cases.

Further robust studies into the phenotypic impacts of these variants, including impacts on epidemiological characteristics (transmissibility, severity, re-infection risk, etc.) and impact on countermeasures, are urgently needed.

WHO COVID-19 Weekly Epidemiological Update –  Data as received by WHO from national authorities, as of 9 May 2021, 10 am CET

 

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

 

Photo by Charlie Costello on Unsplash

WHO: B.1.617 Delta #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.”

WHO: Newly designated VOC within lineage B.1.617 – update on Indian #coronavirus variant

 

UK: surge testing for Delta #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

 

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

 

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

 

Image by David Reed from Pixabay

UK: B.1.617 found in 24% of #coronavirus sequences in Bolton, mostly new Delta 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 Delta #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: double mutant coronavirus variant B.1.617 outcompeting B.1.1.7 UK variant

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

 

Image by Adam Derewecki from Pixabay

B1427/B1429 are listed as Variants of Concern by the CDC, as Variants of Interest (VOI) by WHO

The World Health Organization lists as B.1.427 and B.1.429 as Variants of Interest. The CDC website, however, lists B.1.427 and B.1.429 as Variants of Concern along with B.1.1.7 (UK variant), P.1 (Brazilian Variant) and B.1.351 (South African Variant).

 

CDC:  SARS-CoV-2 Variant Classifications and Definitions

WHO: COVID-19 Weekly Epidemiological Update

 

 

 

Sri Lanka: new SGTF #coronavirus variant appears to have completely displaced B.1.411 within 10 days

Prof. Malavige said that currently, over 95% of the samples from Colombo, Kurunegala and Kalutara give an ‘S drop’, suggesting that these infections are due to this variant [B.1.1.7]. This variant appears to have completely displaced Sri Lanka’s own virus (B.1.411) within a very short period of time (10 days), showing that it is highly transmissible compared to the previous strain.

“There is a strong possibility that a ‘new variant of concern’ of the coronavirus which is highly transmissible and also causing severe disease is currently circulating in Sri Lanka,” said Prof. Neelika Malavige, Head of the Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura.

This variant seems to have displaced the variants of Sri Lankan lineage which have been circulating so far, says Prof. Malavige going onto explain that certain changes are detected in some RT-PCR assays, when there is a variant.

“One of these changes is a so-called ‘S drop’ that occurs due to mutations that are seen in certain variants such as the UK variant (B.1.1.7). However, sequencing or targeted detection of these mutations that occur in these variants is essential to confirm which variant it is. The results of sequencing are expected next week,” she said.

She cautioned that a further COVID-19 blow will come in about 10-14 days, when the number of infected due to disregarding health precautions during avurudu, will surface.

SundayTimes.lk report

See also:

Sri Lanka: new fast spreading #coronavirus strain identified as UK variant B117

Sri Lanka: new fast spreading #coronavirus strain identified as UK variant B117

 

 

Photo by Hendrik Cornelissen on Unsplash

UK SAGE: Lab studies suggest that the N501Y spike protein mutation increases binding to rat and mouse ACE2 leading to viral replication

A report issued by the UK government’s Scientific Advisory Group for Emergencies (SAGE) found the likelihood that a variant of concern (VOC) that has arisen in humans could infect a rodent and then spread among the animals is high. Researchers say lab evidence indicates that while rats and mice appear unable to contract the most common forms of coronavirus COVID-19, the N501Y spike protein mutation “has an increased affinity” for rodents.

The report said: “There is a plausible pathway for infection of rodents with new variants of concern from infected humans following contamination of an environment. “Experimental evidence has shown SARS-CoV-2 with N501Y has increased affinity for lab rodents and there is nothing to suggest the same would not be true for wild rodents.

SAGE: Coronavirus (COVID-19) response, 8 April 2021

 

 

Image by sipa from Pixabay

Brazil: rapid spread and high impact of the #coronavirus VOC P.1 in Sao Paulo – March 2021

Here, we show evidence of how fast the VOC P.1 has spread in the most populated city in South America – Sao Paulo.  From March 1st to March 15th, 427 nasopharyngeal samples were collected from 245 HP and 125 from HCW outpatients (25.5% and 23.2% of positivity rate, respectively). We then selected 60 samples with Ct value ≤ 30 (38 samples from HP, and 22 from HCW). All HCW presented only mild symptoms and did not need hospitalization.

Of the 60 selected samples, 52 whole genome sequences were generated (30 from HP and 22 from HCW) following the sequencing protocol using the Illumina MiSeq platform and the analysis pipeline described by Resende et al (8). The SARS-CoV-2 lineages were classified by the PANGO lineages nomenclature (9). Genome sequences generated have been deposited at the EpiCoV database on GISAID https://www.gisaid.org/) under accession numbers EPI_ISL_1464630 to EPI_ISL_1464677.

Of the 52 sequenced samples, 44 (84.4%) were identified as VOC P.1;  5 (9.2%) as VOI P.2; 1 (1,9%) as B.1.1.7, and 2 (3,8%) B.1.1.28.

The most notable variants circulating in the second wave, including B.1.1.7 (detected first in the United Kingdom) and B.1.1.351 (detected first in South Africa), and P.1, are related to an increase of transmissibility (2,10). Interestingly, the P.1 variant was first identified in the State of Amazonas, about 3,800 kilometers apart from São Paulo (5). It is evident that the P.1 variant prevailed during the first two weeks of March, showing a regular distribution among HP and HCW with no difference in terms of age, sex, vaccination, and outcome (Table). From the first to the second weeks of March, we observed a higher frequency of P.1 (78.6% and 91.7%, respectively). In this survey, only one sample from a HP was identified as VOC B.1.1.7. The other two samples were identified as B.1.1.28, a widely spread lineage during the first wave in Brazil.

There is a broad discussion about whether the available vaccines against SARS-CoV-2 will be less effective at preventing infection with the emerging variants (10). In this work, 14 samples (26.9%) of the 52 sequenced samples were from individuals that had received at least one dose of vaccine, ChAdOx1-S/nCoV-19 (n=2) or SINOVAC (n=26). Although they were vaccinated, they could not be considered immunized, regarding the days after vaccination.

Among the hospitalized patients, 19 (63%) were admitted to the intensive care unit, from which nine were discharged and ten died. Comparing the RT-PCR Ct values of all attended patients since the first wave, we did not observe any difference in the Ct mean values with those of P.1 (data not shown). May 2020 registered the peak of number of positive cases with a Ct mean of 23.6. Now, as of April 2021, we are facing a rise in the number of cases. However, the Ct mean was 24.9, which may indicate that the spread of P.1 does not contribute to an actual increase in the viral load.

Medrixiv preprint

 

Image by Luciano Teixeira from Pixabay

CDC: SARS-CoV-2 #Coronavirus Variant Classifications and Definitions including Variant of Interest (VOI), Variant of Concern (VOC) & Variant of High Consequence (VHC)

Variant of High Consequence (VHC): A variant of high consequence has clear evidence that prevention measures or medical countermeasures (MCMs) have significantly reduced effectiveness relative to previously circulating variants.

Variant of Concern (VOC): A variant for which there is evidence of an increase in transmissibility, more severe disease (increased hospitalizations or deaths), significant reduction in neutralization by antibodies generated during previous infection or vaccination, reduced effectiveness of treatments or vaccines, or diagnostic detection failures.

Variant of Interest (VOI): A variant with specific genetic markers that have been associated with changes to receptor binding, reduced neutralization by antibodies generated against previous infection or vaccination, reduced efficacy of treatments, potential diagnostic impact, or predicted increase in transmissibility or disease severity.

CDC list of VOI’s, VOC’s and VHC’s