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B.1.640: 5 Canadian cases of little-known coronavirus variant

TORONTO — A coronavirus variant that made headlines recently has been a “variant under monitoring” since November 2021, according to the World Health Organization (WHO), but is not currently circulating widely.

The B.1.640 variant was first detected in a number of countries in September 2021, according to the WHO, and has two sub-lineages, B.1.640.1 and B.1.640.2. B.1.640.2, dubbed the “IHU” following a study published at the end of December on the preprint server medRxiv.org by IHU Méditerranée Infection in Marseille, France, attracted attention due to the large number of mutations detected. Preprints are studies that have yet to be peer-reviewed and evaluated.

Five cases of the variant have been sequenced in Canada and shared on GISAID – four in Ontario and one in Quebec. GISAID allows scientists from around the world to quickly share COVID-19 data, including genetic sequencing. The Quebec sequence was collected on Oct. 2, 2021 in a 34-year-old individual. One Ontario sample was collected in a male on Dec. 10, 2021 and another on Jan. 4, according to GISAID data.

Variants under monitoring are those with genetic changes that are “suspected to affect virus characteristics with some indication that it may pose a future risk” but the evidence of its impact is currently unclear, according to the WHO. These variants fall below the “variants of concern” identified by the health agency, such as Omicron and Delta, and also below “variants of interest” which have genetic changes predicted or known to affect characteristics like transmissibility and disease severity, and has caused notable transmission or clusters in multiple countries or other epidemiological impacts that could pose a risk.

“Less than one per cent of the samples that were sequenced in France are of this particular variant,” Dr. Maria Van Kerkhove, the COVID-19 technical lead with the World Health Emergencies Programme said during a WHO press conference.

“This means that it’s important that we track this, particularly because of the number of mutations that it has, but it isn’t circulating widely at the moment.”

Globally, focus remains on the Omicron variant that has swept through at least 99 countries with unprecedented speed. Unlike the B.1.640 variant, Omicron, which also carries a large number of mutations, has pushed daily new infections to record-breaking levels in numerous countries.

“[B.1.640] is just something to keep an eye on. It looks like it’s being overcrowded by Omicron and it doesn’t look like this has taken off, but obviously you can’t sweep anything under the rug,” infectious diseases specialist Dr. Isaac Bogoch told CTV’s Your Morning earlier this week.

“This variant was discovered in September and it hasn’t exploded yet in France or elsewhere in the world. Again, you can’t ignore it, but it’s pretty clear that Omicron is the current and significant threat right now and we really have to take Omicron seriously.”

Van Kerkhove emphasized the continued importance of sharing sequencing on global platforms like GISAID to help track the variants. In December alone, an unprecedented one million genetic sequences were shared on the platform, she said.

“The reason why we classify it as a variant under monitoring is to raise awareness and for people to be on the lookout for that,” she added.

Most of the B.1.640 sequences reported on GISAID have come from France, with 319, followed by Republic of the Congo, with 40.

The B.1.640.2 lineage has 46 mutations and 37 deletions resulting in 30 amino acid substitutions and 12 deletions, according to the IHU pre-print, with 14 amino acid substitutions and 9 deletions located in the spike protein. 

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