French health authorities detect new Covid-19 variant 'IHU'
05 January 2022
Amid the scare over the fast-spreading SARS-CoV variant Omnicron, first reported from South Africa, researchers in France have detected a new variant of the virus, believed to be originated in Cameroon, in central Africa.
The new variant, which the researchers have temporarily named as 'IHU', is of the B.1.640.2 lineage and is believed to have infected 12 people in the country, according to a French government supported study.
"For twelve SARS-CoV-positive patients living in the same geographical area of south-eastern France, qPCR testing that screen for variant-associated mutations showed an atypical combination," reports quoted Philippe Colson, from IHU Mediterranee Infection, Marseille, as saying.
However, he said, "it is too early to speculate on virological, epidemiological or clinical features of this IHU variant based on these 12 cases."
The first patient detected to have been infected with the `IHU; variant, was a vaccinated adult who had returned to France from a trip to Cameroon.
Three days after returning he developed mild respiratory symptoms. His nasopharyngeal sample collected in 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 was quoted as saying.
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 stated.
"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, adding 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," Colson said.
"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," he said.