SARS-CoV-2 Variants - Coronavirus COVID-19 **NO DISCUSSION**

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Statement on new SARS-CoV-2 variant with multiple spike protein mutations – Africa CDC
22 DECEMBER 2020

“ADDIS ABABA, ETHIOPIA, 22 DECEMBER 2020. The Africa Centres for Disease Control and Prevention (Africa CDC) wishes to raise awareness of Member States regarding the new variant of SARS-CoV-2, the virus that causes COVID-19, which was reported in South Africa and the United Kingdom over the past week. Africa CDC is closely following up with authorities in South Africa, where the variant was first identified in Nelson Mandela Bay and has rapidly spread through the Eastern and Western Capes, as well as KwaZulu-Natal.

This new variant is defined by multiple non-synonymous mutations in the spike (S) protein. Three of these mutations are located on the receptor-binding domain (RBD) of the spike protein – the most notable being the N501Y mutation on the receptor binding motif that binds to the human Angiotensin Converting Enzyme-2 (ACE2) receptor.

Preliminary analyses from South Africa and the United Kingdom suggest that this new variant may be associated with increased transmissibility and a higher viral load than the previously circulating variants.

However, researchers are conducting further investigations on this new N501Y variant to determine if it is more infectious, more transmissible, or has the potential to cause more severe illness. Research is also being conducted to assess the impact of the mutations on the performance of existing molecular diagnostics, serological assays, therapeutics, and vaccines.”

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“On 21 December, Africa CDC convened an emergency meeting of the Africa Taskforce on Coronavirus Response (AFTCOR), where the Network for Genomics Surveillance in South Africa, led by Prof. Tulio de Olivera and Prof. Salim Abdool Karim, shared findings from South Africa. The meeting discussed what is known, what is not known, and what needs to be done about this new variant. The Taskforce recommends the following:

  • Africa CDC Institute for Pathogen Genomics (IPG) should immediately coordinate further actions by a continental network of clinical laboratory centres of excellence to enhance surveillance of the new variant virus.
  • Member States should enhance implementation of ongoing public health and social measures to prevent further transmission of COVID-19, including correct and consistent mask-wearing, physical distancing and hand hygiene.
  • There is no immediate need to restrict trade and travel across the continent, because travellers across the continent now require a negative virologic test (PCR or Antigen test) before they can travel.
  • All stakeholders should support and contribute to the rapid sharing of data across the continent.“
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“Recommendations to Member States and health authorities

Coincidentally, the news of this variant has come when the continent is also experiencing a second wave of the COVID-19 pandemic. Therefore, Africa CDC advises that Member States reinforce their efforts to increase testing, contact tracing and early treatment of cases while we seek to gain more insight about the impact this new variant could have on testing accuracy, clinical outcomes and vaccine efficacy.

Specifically, we recommend that:

  1. Member States increase general awareness of the new variant and take timely measures to monitor, prevent and control its spread.
  2. Public health laboratories and researchers should strengthen collaboration and coordination with national and regional pathogen genomics laboratories in order to conduct genomic surveillance and sequencing of the virus in a timely manner. The Africa CDC IPG, through the Africa Pathogen Genomics Initiative, will support this coordination at the continental level.
  3. Member States should notify Africa CDC immediately if they identify any new SARS-CoV-2 variant.
  4. Member States should enhance community-based surveillance for early identification of hotspots and continue to encourage community members to adhere to public health and social measures for their protection.
  5. Member States and Africa CDC Regional Collaborating Centres should enhance surveillance and cross-border health measures at ports of entry, but there is no immediate need for restrictions on travel and trade.
Africa CDC will continue to monitor the situation and provide updates to Member States and the public as more information becomes available about this SARS-CoV-2 variant.“

—

Additional resources

Information on the U.K. lineage is available the COVID-10 Genomics UK Consortium Website (https://www.cogconsortium.uk/news/) and on virological.org website (Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations)
 
Osterholm Update: COVID-19 |Episode 37: Now Is the Time | December 23. 2020

“In this episode, Dr. Osterholm and host Chris Dall discuss reports of new SARS-CoV-2 variants from the UK and South Africa and potential implications, additional federal recommendations for vaccine prioritization, further information on vaccines for pregnant women, and the epidemiology of the pandemic heading into the holidays.“

 
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Multiple countries report UK SARS-CoV-2 variant cases
Dec 28, 2020


“Scientists rush to see how variants behave
At a World Health Organization (WHO) briefing today, Maria Van Kerkhove, PhD, the group's technical lead for COVID-19, said the WHO is in touch with UK officials daily and that researchers were working over the holidays on lab studies to learn more about the variant viruses, including antibody response. She said a new case control study from the UK suggests that there are no differences in hospitalizations, case-fatality rates over 28 days, or reinfections.

Van Kerkhove also said South African researchers are currently growing the virus to enable neutralization and other studies and that officials are also examining the epidemiology of illnesses involving the new variant.

"Lab studies take time, and we expect more info on both in the coming days and weeks," she said.

In a Dec 23 preprint study, researchers from the UK estimated that the variant is 56% more transmissible, which is likely to lead to a large increase in incidence, with hospitalizations and deaths likely to reach even higher levels. However, they didn't find clear evidence that the variant's severity is any different than those of existing viruses.

In wake of variants, cases soar in UK and South Africa
Meanwhile, the UK today reported a new record single-day high of 41,385 cases. In a statement, Yvonne Doyle, MD, MPH, Public Health England's (PHE's) medical director, said, "This very high level of infection is of growing concern at a time when our hospitals are at their most vulnerable, with new admissions rising in many regions." A few days ago PHE said lateral flow tests can detect the new UK variant.

In South Africa, where cases area also soaring, President Cyril Ramaphosa today announced new restrictions on gatherings, a new curfew, and a ban on alcohol sales," according to the BBC. He said the country is at a dangerous point in the pandemic and that hospitals and medical centers are reporting large rises in admissions.

WHO officials today emphasized that reducing transmission gives the virus fewer opportunities to change and that making the best use of current measures such as physical distancing, face masks, and now vaccination can help reduce the spread of the variant viruses. Van Kerkhove said the variant developments are another wake-up call that the world needs even more resolve to battle COVID-19. "I know we are all fed up, but we can't lose this battle now," she said. "We need to put in the work to reduce risk everywhere we can."”
 
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AstraZeneca: Shot will be effective against COVID-19 variant
December 27, 2020

“LONDON (AP) — The head of drugmaker AstraZeneca, which is developing a coronavirus vaccine widely expected to be approved by U.K. authorities this week, said Sunday that researchers believe the shot will be effective against a new variant of the virus driving a rapid surge in infections in Britain.

AstraZeneca chief executive Pascal Soriot also told the Sunday Times that researchers developing its vaccine have figured out a “winning formula” making the jab as effective as rival candidates.

Some have raised concern that the AstraZeneca vaccine, which is being developed with Oxford University, may not be as good as the one made by Pfizer already being distributed in the U.K. and other countries. Partial results suggest that the AstraZeneca shot is about 70% effective for preventing illness from coronavirus infection, compared to the 95% efficacy reported by Pfizer and its German partner BioNTech.“
 
December 27, 2020

*Dr. Gottlieb says that the US doesn’t do a lot of genomic sequencing. That which is done is done in private labs, and doesn’t get aggregated to public databases - “This needs to be fixed”. UK sequences about 10% of samples, compared to the US, which only sequences a fraction of one percent - a “better approach“ is needed to systematically sequence and track changes and variants in this virus.

 
Explainer: The new coronavirus variant in South Africa - Are concerns justified?
December 25, 2020

“It has also been associated with a higher viral load, meaning a higher concentration of virus particles in patients’ bodies, possibly contributing to higher levels of transmission.

Between 80% and 90% of new cases in the country are carrying the mutant variant, according to health authorities.”
 
WHO Director-General's opening remarks at the media briefing on COVID-19 - 28 December 2020

28 December 2020 | transcript source | full conference

“Specifically we are working with scientists in the UK and South Africa who are carrying out epidemiologic and laboratory studies, which will guide next steps.

Science drives our actions.

I would like to thank both those countries for testing and tracking new variants and underscore the importance of increasing genomic sequencing capacity worldwide.

This means the prompt sharing of epidemiological, virological, and full genome sequence information with WHO and other countries and research teams, including through open-source platforms such as GISAID and others.

Only if countries are looking and testing effectively will you be able to pick up variants and adjust strategies to cope.

We must ensure that countries are not punished for transparently sharing new scientific findings.“
 
Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England
23-12-2020

A novel SARS-CoV-2 variant, VOC 202012/01, emerged in southeast England in November 2020 and appears to be rapidly spreading towards fixation. We fitted a two-strain mathematical model of SARS-CoV-2 transmission to observed COVID-19 hospital admissions, hospital and ICU bed occupancy, and deaths; SARS-CoV-2 PCR prevalence and seroprevalence; and the relative frequency of VOC 202012/01 in the three most heavily affected NHS England regions (South East, East of England, and London). We estimate that VOC 202012/01 is 56% more transmissible (95% credible interval across three regions 50-74%) than preexisting variants of SARS-CoV-2. We were unable to find clear evidence that VOC 202012/01 results in greater or lesser severity of disease than preexisting variants. Nevertheless, the increase in transmissibility is likely to lead to a large increase in incidence, with COVID-19 hospitalisations and deaths projected to reach higher levels in 2021 than were observed in 2020, even if regional tiered restrictions implemented before 19 December are maintained. Our estimates suggest that control measures of a similar stringency to the national lockdown implemented in England in November 2020 are unlikely to reduce the effective reproduction number Rt to less than 1, unless primary schools, secondary schools, and universities are also closed. We project that large resurgences of the virus are likely to occur following easing of control measures. It may be necessary to greatly accelerate vaccine roll-out to have an appreciable impact in suppressing the resulting disease burden.

Read the full preprint here.

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CDC | New Variant of Virus that Causes COVID-19 Detected
Updated Dec. 28, 2020

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Multiple countries report UK SARS-CoV-2 variant cases
Dec 28, 2020
CIDRAP

“Variant detected in multiple countries
Following the recent detection of the more-transmissible UK variant, several more countries spanning multiple continents reported their first detections over the weekend, triggering more travel bans and other related measures to slow the spread.

In North America, the Public Health Agency of Canada on Dec 26 reported two cases in Ontario, both in people who did not travel outside of Canada. The country extended its ban on flights from the UK until Jan 6.

At least 14 other countries over the past few days reported similar cases, according to official sources and media reports, including France, Japan, Denmark, South Korea, Finland, Sweden, Spain, Switzerland, the Netherlands, Germany, Italy, Lebanon, Singapore, and Australia.

Some countries also reported their first detections of a similar South African variant, including the UK and Finland.

In other variant developments, another new variant has been reported from Nigeria, according CBS News. John Nkengasong, PhD, of the Africa Centers for Disease Control and Prevention said further investigation is under way by Nigerian scientists and those at the African Center of Excellence for Genomics of Infectious Diseases.”
 
COVID-19 IN COLORADO: COVID-19 variant from U.K. discovered in Colorado
Dec 29, 2020

DENVER (KDVR) — A variant of COVID-19 first discovered in the United Kingdom has now been discovered in Colorado.

The Colorado State Laboratory said the person is a man in his 20s who is currently in isolation in Elbert County and has no travel history.
...

“The fact that Colorado has detected this virant first in the nation is a testament to the sophistication of Colorado’s response and the talent of CDPHE’s scientist and lab operations,” said Jill Hunsaker Ryan, executive director, Colorado Department of Public Health and Environment.
 
WHO Conference: Dr. Maria talks about how there is a whole group/team which was set up in January, whose chief purpose is to monitor, study and track the evolution of the virus - mutations, strains, variants, etc.
 
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