FRANCE : Covid-19 variant B.1.640 has some unprecedented mutations that allows the virus to cling to the human cell and start the infection process

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A new COVID variant identified in a handful of European countries is raising concerns among some health professionals because there are changes to the coronavirus spike protein that have never been seen before.

The variant, known either as B.1.X or B.1.640, was first reported by the French paper Le Telegramme after it infected 24 people at a French school in the Brittany region last month.

When the variant was discovered in France, the school at which the outbreak occurred was forced to close half of its classes, Le Telegramme reported.

Although the situation is now under control and no cases have been found in France since October 26, the French Regional Health Agency said, the variant remains under surveillance.

Currently designated Variants of Concern (VOCs)+:

WHO label Pango  
lineage*
GISAID cladeNextstrain clade Additional amino acid changes monitored°Earliest documented  
samples 
Date of designation 
Alpha B.1.1.7 GRY20I (V1) +S:484K
+S:452R
United Kingdom,  
Sep-2020 
18-Dec-2020
Beta B.1.351 GH/501Y.V2 20H (V2)+S:L18FSouth Africa,  
May-2020 
18-Dec-2020
Gamma P.1 GR/501Y.V3 20J (V3)+S:681HBrazil,  
Nov-2020 
11-Jan-2021
Delta B.1.617.2G/478K.V1 21A, 21I, 21J+S:417N+S:484KIndia,  
Oct-2020 
VOI: 4-Apr-2021 
VOC: 11-May-2020
Omicron*B.1.1.529GR/484A21KMultiple countries, Nov-2021VUM: 24-Nov-2021VOC: 26-Nov-2021
source :https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/

Currently designated Variants of Interest (VOIs):

WHO label Pango  
lineage*
GISAID cladeNextstrain  
clade 
Earliest documented  
samples 
Date of designation 
LambdaC.37GR/452Q.V121GPeru, Dec-202014-Jun-2021
MuB.1.621GH21HColombia, Jan-202130-Aug-2021
source :https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/

Currently designated Variants Under Monitoring

Pango  
lineage* 
GISAID cladeNextstrain  
clade 
Earliest documented  
samples 
Date of designation 
AZ.5#GRMultiple countries,
Jan-2021
VUM: 02-Jun-2021
C.1.2GRSouth Africa, May 202101-Sep-2021
B.1.617.1§ G/452R.V3 21BIndia, Oct-2020  VOI: 4-Apr-2021 VUM: 20-Sep-2021
B.1.526§  GH/253G.V121F United States of America,  Nov-2020 VOI: 24-Mar-2021 VUM: 20-Sep-2021 
B.1.525§ G/484K.V3 21DMultiple countries, 
Dec-2020 
VOI:17-Mar-2021VUM: 20-Sep-2021 
B.1.630GHDominican Republic, Mar-202112-Oct-2021
B.1.640GH/490RRepublic of Congo, Sep-202122-Nov-2021
source :https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/

Formerly monitored variants

Pango  
lineage* 
GISAID cladeNextstrain  
clade 
Earliest documented  
samples 
Date of designation 
AV.1 GRUnited Kingdom, Mar-2021 VUM: 26-May-2021Reclassified: 21-Jul-2021 
AT.1 GRRussian Federation, Jan-2021 VUM: 09-Jun-2021 Reclassified: 21-Jul-2021 
P.2§GR/484K.V2 20B/S.484K  Brazil, Apr-2020  VOI: 17-Mar-2021 VUM: 6-Jul-2021  Reclassified: 17-Aug-2021 
P.3§GR/1092K.V121EPhilippines, Jan-2021VOI: 24 Mar 2021VUM: 6 Jul 2021Reclassified: 17-Aug-2021 
R.1GRMultiple countries, Jan-2021VUM: 07-Apr-2021Reclassified: 9-Nov-2021  
B.1.466.2 GHIndonesia, Nov-2020VUM: 28-Apr-2021 Reclassified: 9-Nov-2021 
B.1.1.519GR20B/S.732AMultiple countries, Nov-2020VUM: 02-Jun-2021Reclassified: 9-Nov-2021 
C.36.3GRMultiple countries, Jan-2021VUM: 16-Jun-2021Reclassified: 9-Nov-2021 
B.1.214.2GMultiple countries, Nov-2020VUM: 30-Jun-2021Reclassified: 9-Nov-2021 
B.1.427B.1.429§GH/452R.V1  21CUnited States of America, Mar-2020 VOI: 5-Mar-2021 VUM: 6-Jul-2021Reclassified: 9-Nov-2021 
B.1.1.523GRMultiple countries, May-2020VUM:14-July-2021Reclassified: 9-Nov-2021 
B.1.619G20A/S.126AMultiple countries, May-2020VUM:14-July-2021Reclassified: 9-Nov-2021 
B.1.620GMultiple countries, Nov-2020VUM:14-July-2021 Reclassified: 9-Nov-2021 
source :https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/

Where was the B.1.640 variant detected?

“The B.1.640 variant was detected 11 times in France, including 8 cases confirmed by sequencing as part of the investigation of a cluster in Brittany; the index case of this cluster had a history of travel to the Republic of Congo” , notes the CNR in its latest risk analysis published this weekend . 

It could also have been detected sporadically in Provence-Alpes-Côte d’Azur as well as in Ile-de-France, without this information being confirmed yet.  

Internationally, B.1.640 appeared for the first time in Congo, in September. The very first case to appear in Brittany would have been imported by a person returning from this country located on the African continent. 

Sequences carrying this variant have also been spotted once in Italy, the Netherlands, Switzerland, the United Kingdom, as well as in the United States. 

A handful of cases were also discovered in the United Kingdom, Switzerland, Scotland and Italy, although the Delta variant and its descendants continue to be the most dominant strains.

Bar-Ilan University Prof. Cyrille Cohen, who is originally from France and regularly interviews and consults with French health officials, explained that the B.1.640 variant has some unprecedented mutations.

One in particular has drawn attention: the spike protein, which is what allows the virus to cling to the human cell and start the infection process, has some deletions.The question is whether this will make the virus more or less infectious.

The variant is believed to have emanated from Africa, a scenario Cohen said health experts are afraid of and that highlights the need for vaccine equality.

“This variant exemplifies that if you leave some of the world’s population without access to vaccines, then the virus will continue to multiply and it will lead to more variants,” Cohen said.

A Q4 Global Forecast report published last week by the Economist Intelligence Unit (EIU) highlighted that while mostly developed countries have successfully vaccinated large swaths of their citizens, most developing countries have made only negligible progress.

The report specifically highlighted the failures of Africa’s vaccination drive, where as of late October only 6% of the population in African states is vaccinated against COVID.

“The cause of such low vaccination rates is well-known: Despite recent improvements, global production continues to lag behind demand, with developing countries facing long delays in accessing vaccines,” the EIU report said, adding that the World Health Organization’s COVAX program has only managed to ship some 400 million doses globally and that donations from richer countries have been sparse.

Moreover, even if vaccines were delivered, African countries would be challenged in rolling them out, the report said – mainly for logistical reasons.

“Not giving vaccines to these countries may seem OK in the short term,” Cohen said, “but in the long term, we might have new variants that are problematic that developed in unvaccinated countries.”

“I don’t want to frighten people,” he said. “There are just a few cases of B.1.640 now and it could very well be that in a month we could all forget about this variant.
“But it is an example of what could happen if there isn’t access to vaccines for everyone.”

What are its characteristics ?

The CNR noticed in B.1.640 an “unusual” profile of mutations – nine in all – affecting the S protein (Spike), the one that allows the virus to enter our cells. The best known, N501Y, present in the Alpha, Beta and Gamma variants, makes the variant more transmissible.  

Another deletion, 137-145, “could result in decreased neutralization by post-infection or post-vaccine neutralizing antibodies”. In short, B.1.640 would be able to alter the efficacy of the sera injected so far, or to decrease the natural immunity acquired after contracting the disease.  

The CNR remains confident: this mutation has already been observed in variants such as Alpha and Eta, without “any major vaccine escape” being observed. “Its impact remains to be evaluated,” concludes the Reference Center, which also mentions the presence of P681H mutations – which induces greater infectivity – as well as T859N. 

Is it considered dangerous?

Public Health France and the CNR reassure: “The epidemiological data show the absence of significant dissemination or progression in France or internationally. There are no convincing virological, epidemiological or clinical elements in favor of an impact significant in public health, ”they note. “The presence of mutations shared with one or more VOC / VOI variants (VOC: variants of concern / VOI: variants to follow, NDLR) is however to be monitored.” 

Scientists remain on the alert. “We wonder how it is possible for a variant to appear in so many countries. Is it simply because travelers move around or because it has particular characteristics?” Asks Etienne Simon-Lorière, responsible for the evolutionary genomics unit of RNA viruses at the Institut Pasteur, in the columns of the Parisien . In Congo, the sequences of this mutation are more numerous than those linked to the Delta variant, the majority across the globe. 

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