January 05, (THEWILL) – While the world is grappling with the highly infectious Omicron strain of COVID-19, scientists in France have identified a new coronavirus strain, B.1.640.2, at the institute IHU Méditerranée Infection in Marseille.
Named IHU, the new B.1.640.2 variant has so far infected 12 people living in southeastern France. The first case was linked to a person with a travel history to Cameroon.
This is coming some days after Israel reported its first case of rare double infection of COVID and Influenza, Flurona.
Although it is yet to be spotted in other countries or labelled a variant under investigation by the World Health Organisation (WHO), researchers believe the new variant contains 46 mutations, more than Omicron.
Prof Philippe Colson, who heads the unit that discovered the strain, said: “We indeed have several cases of this new variant in the Marseille geographical area. We named it ‘variant IHU’. Two new genomes have just been submitted. It is too early to speculate on virological, epidemiological or clinical features of this IHU variant based on these 12 cases.”
According to the study, the index case (the first patient) was a vaccinated adult who had returned to France from a trip to Cameroon, in central Africa.
Three days after returning, he developed mild respiratory symptoms. His nasopharyngeal sample collected mid-November 2021, “revealed an atypical combination that did not correspond to the pattern of the Delta variant involved in almost all SARS-CoV-2 infections at that time”, and later to Omicron as well, Colson said.
Respiratory samples collected from seven other SARS-CoV-2-positive patients living in the same geographical area exhibited the same combination of mutations screened by qPCR. They were two adults and five children (below 15 years of age).
The respiratory samples from these eight patients were sent to university hospital institute Mediterranee Infection for SARS-CoV-2 genome sequencing as recommended by French public health authorities.
Further tests led to SARS-CoV-2 genotype identification. The analysis revealed 46 mutations and 37 deletions resulting in 30 amino acid substitutions and 12 deletions. Fourteen amino acid substitutions, including N501Y and E484K, and 9 deletions are located in the spike protein.
“This genotype pattern led to create a new Pangolin lineage named B.1.640.2, which is a phylogenetic sister group to the old B.1.640 lineage renamed B.1.640.1. Both lineages differ by 25 nucleotide substitutions and 33 deletions,” the study said.
“The mutation set and phylogenetic position of the genomes obtained here indicate, based on our previous definition, a new variant we named ‘IHU”, Colson said.
He added that the data is “another example of the unpredictability of the emergence of SARS-CoV-2 variants. Overall, these observations show once again the unpredictability of the emergence of new SARS-CoV-2 variants and their introduction from abroad, and they exemplify the difficulty to control such introduction and subsequent spread.
“SARS-CoV-2 variants have become a major virological, epidemiological and clinical concern, particularly with regard to the risk of escape from vaccine-induced immunity. The emergence of the new variant warrants the increase of genomic surveillance of SARS-CoV-2.”
The report of the new variant came after French health minister Olivier Veran said that the country expects to see even higher daily counts of new COVID-19 infections.
Last week, France saw four consecutive days of record-breaking new cases above 200,000. Veran had added that the number might go as high as 300,000 to 400,000 in the coming days.
“I said that maybe – maybe – this is the last wave, meaning that considering the number of infections in our country and around the world, it’s probable that we will have developed a form of immunity, either through vaccination or through getting infected, or both” he said.
U.S. epidemiologist and health economist, Eric Feigl-Ding, who alerted to the variant, said: ‘’These observations show once again the unpredictability of the emergence of new #SARSCoV2 variants and they exemplify the difficulty to control such introduction and subsequent spread.
“However, it does not mean they will be more dangerous. What makes a variant more dangerous is its ability to multiply because of the number of mutations it has in relation to the original virus.
“This is when it becomes a variant of concern like Omicron, which is more contagious and could evade immunity. It remains to be seen in which category this new variant will fall.”
Researchers noted that it is too early to speculate on how this variant behaves as far as infection and protection from vaccines is concerned.
According to the researchers, the index (first) case was an adult diagnosed positive in mid-November last year.
Many countries are currently experiencing a spike in COVID-19 cases driven by the Omicron variant, which was first identified in South Africa and Botswana in November last year. Since then, the variant of concern has spread to over 100 countries.
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