UK: PHE Technical Briefing and Variants of Concern update 18

PHE England have recently published new reports on the SARS-COV-2 variants circulating in Britain: Alpha, Beta, Gamma, Zeta, Eta, B.1.1.318, Theta, Kappa, B.1.617.3, AV.1, C.36.3, Lambda, C.37

SARS-CoV-2 variants of concern and variants under investigation in England

Variants under surveillance
Variant prevalence
Secondary attack rates
SARS-CoV-2 Immunity and Reinfection Evaluation (the SIREN study) cohort monitoring

Part 2: Delta (B.1.617.2) surveillance
Surveillance through genomic data
Delta with K417N (Delta-AY.1)

 

Investigation of SARS-CoV-2 variants of concern: routine variant data update

Data on individual variants
Alpha
Beta
Gamma
International Epidemiology
Zeta
Eta
VUI-21FEB-04 (B.1.1.318)
Theta
Kappa
VUI-21APR-03 (B.1.617.3)
VUI-21MAY-01 (AV.1)
VUI-21MAY-02 (C.36.3)
Lambda (C.37, VUI-21JUN-01)

 

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

Australia: “non-infectious chronic shedder” tests positive after discharge from #coronavirus quarantine hotel

Australian health authorities are contacting scores of people in Western Australia after a man tested positive to COVID-19 after being released from the state’s quarantine hotels. Western Australia Chief Health Officer Dr Andrew Robertson said “We often get people who are chronic shedders, but the test result was more moderately positive than we would anticipate. So, as a precaution, we have put him back into one of the quarantine hotels and have taken further tests.”

“His test today was weaker which is more in line with what we would expect with somebody who was a chronic shedder and we believe that he is a non-infectious chronic shedder”.

Image by Karenlaptop from Pixabay

Vietnam: No new hybrid #coronavirus strain detected in Vietnam says WHO

“There is no new hybrid variant in Vietnam at this moment based on WHO definition,” Kidong Park, the WHO representative in Vietnam, told Nikkei Asia on Wednesday. “The variant detected is Delta variant (B.1.617.2), with additional mutations, and needs more observation. We need to monitor during next couple of weeks,”

“This is within the existing [Delta] variant. It is an additional mutation” Park explained, adding “as for now, there is no alarming alert from WHO. Park also stressed the Delta variant is dangerous as it is highly contagious and spreads very quickly.

Nikkei Asia report

 

Vietnam: recombinant/hybrid #coronavirus announced – B.1.617.2 Delta variant with Y144 mutation from B.1.1.7 Alpha variant

 

Vietnam: Young #coronavirus patients with no underlying health conditions have ‘white lungs after a few days of Covid-19 symptoms’

 

 

Photo by Ammie Ngo on Unsplash

WHO announce new names for Sars-CoV-2 #coronavirus variants

The WHO have announced new names for the confusingly named sars-cov-2 variants. The new names are based on the Greek alphabet.

Variants of Concern = Alpha, Beta, Gamma, Delta

 

Variants of Interest = Epsilon, Zeta, Eta, Theta, Iota, Kappa

 

WHO introduces new naming system for Sars-CoV-2 variants based on Greek alphabet –  Alpha, Beta, Gamma, Delta, Epsilon, Zeta, Eta, Theta, Iota, Kappa etc

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

UK: 487 reinfections for UK #coronavirus variant B.1.1.7 and 13 reinfections already for B.1.617.2

The latest UK PHE technical report shows that there have been 487 cases of reinfection recorded for the UK variant B.1.1.7. There have already been 13 reinfections for the newly announced Indian VOC variant B.1.617.2.

 

UK PHE: SARS-CoV-2 variants of concern and variants under investigation in England, Technical briefing 11

 

Mink: 100% infection, recovery and then 75% re-infection of farmed mink

 

Cameroon: travel-driven emergence and spread of SARS-CoV-2 lineage B.1.620 with multiple VOC-like mutations and deletions in Europe

“In this study we have presented evidence that a SARS-CoV-2 lineage designated B.1.620, first detected in Europe in late February, is associated with Central Africa, where it appears to circulate at very high prevalence, and has been introduced into Europe and the US on multiple occasions. A fair number of known B.1.620 genomes that were sequenced in Europe stem from travel-related cases returning from Cameroon, suggesting that it is likely to be the immediate source of this lineage.”

VOC amino acid changes lineage B.1.620 shares most in common with:

B.1.1.7 (ORF1a: SGF3675/3677Δ, S:Y144Δ, S: HV69/70Δ, S: P681H, and S: D1118H)

P.1 (ORF1a: SGF3675/3677Δ, S:P26S, S:E484K, S: T1027I) and

B.1.351 (ORF1a: SGF3675/3677Δ, S: E484K, S: LLA241/243Δ)

MedrXiv preprint Travel-driven emergence and spread of SARS-CoV-2 lineage B.1.620 with multiple VOC-like mutations and deletions in Europe

 

 

Image by rem734 from Pixabay

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: Delta #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 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

Nepal: highest-ever number of new #coronavirus cases in last 24 hours at 9,196

Nepal recorded a total of 9,196 new cases of coronavirus infection in the past 24 hours. According to the Ministry of Health and Population, 9,023 persons have been tested positive for COVID-19 through the RT-PCR method while 173 have been tested positive through the Antigen method. According to the Ministry, 3,089 persons in Kathmandu, 643 in Lalitpur, and 374 in Bhaktapur have been tested positive for the pandemic virus, making the capital valley’s fresh coronavirus cases 4,106 in past 24 hours.

According to the Ministry, 50 people have succumbed to COVID-19 related death in past 24 hours taking the death tally to 3,579 as of Friday afternoon.

Kharbahub.com report

Nepal: rise in #coronavirus cases has similar trajectory to India driven by B117 and B1617

Nepal: rise in #coronavirus cases has similar trajectory to India driven by B117 and B1617

Graph courtesy of OurWorldInData.org