Scientists have examined the Nextstrain and GISAID databases and found that the L452R mutation is present in more than 400 SARS-CoV-2 genomes isolated from over 20 countries. This indicates a strong positive selection for L452R mutation.
The scientists identified L452R amino acid substitution in the spike region as the dominant mutation in specimens collected since November 2020. Specifically, they observed that two independent SARS-CoV-2 variants (CAL.20C and CAL.20A) containing spike L452R mutation emerged recently in the state of California. Of these variants, CAL.20C (clade 20C; lineage B.1.429) is considered to be the predominant variant in California since November 2020. However, the CAL.20A variant (clade 20A; lineage B.1.232) identified in this study has emerged much more recently than CAL.20C and is primarily circulating in California. Based on the phylogenetic analysis, the scientists indicated that L452R mutation is the primary driving force behind the emergence of both variants. Such an increase in L452R mutation frequency in recent SARS-CoV-2 variants directly indicates its crucial involvement in viral adaptive evolution due to positive selection.
Interestingly, they found CAL.20A variant from a gorilla at the San Diego Zoo, which contains two additional mutations in the non-structural protein 2 (NSP2).
In contrast to CAL.20C, no massive clonal expansion was observed for CAL.20A. According to the study findings, CAL.20C contains two additional spike mutations along with L452R, which are missing in CAL.20A. The scientists believe that these additional mutations may be responsible for increasing the adaptive benefits of L452R, and because of this reason, CAL.20A could not achieve the same expansion rate as CAL.20C.
194 new deaths and nearly 43,000 new cases reported today, Contamination and the number of patients in intensive care remain at high levels, confirming the arrival of a third epidemic wave announced by Olivier Véran.
Researchers plead for a month of strict containment. The prospect of a strict and generalized reconfinement resurfaces due to the hospital tension. Researchers and doctors plead for long-term measures.
Mircea Sofonea, lecturer in epidemiology at the University of Montpellier (Hérault), is on the same line. “According to my models, it would be necessary to confine strictly, as in March 2020, at least for six weeks, judges this specialist. This deadline would make it possible to find an incidence rate below 5,000 new cases per actual day, the threshold set by Emmanuel Macron in November to accept deconfinement. We would also arrive at less than 2000 patients in intensive care and a less active circulation of the virus. It all depends on the health objectives set, in particular at the level of hospital occupation. Currently, Covid-19 patients are being cared for at the expense of deprogrammed patients. We will then have to catch up. ”
Variant de clade 20C ayant émergé en Bretagne
Un cluster d’infections par un variant de clade 20C (« variant 20C/H655Y »), a été détecté dans un hôpital des Côtes d’Armor, avec des cas survenus entre janvier et mars 2021. La particularité associée aux premiers cas confirmés d’infections à ce variant est la possibilité de présenter des symptômes évocateurs de la COVID-19 avec une RT-PCR faiblement positive, voire négative, sur les prélèvements naso-pharyngés habituels.
Le virus est néanmoins détectable par les techniques de PCR habituelles mais semble être retrouvé de manière préférentielle dans les voies aériennes basses. À ce jour, il n’est pas démontré que ce variant serait plus transmissible ni qu’il entraînerait de formes plus sévères, mais son émergence fait l’objet d’investigations et la situation est suivie sur le territoire via une surveillance spécifique. En cas de suspicion d’infection à ce variant (définition de cas et conduite à tenir, disponibles sur le site internet de Santé publique France), des prélèvements au-delà de la sphère naso-pharyngée chaque fois que possible doivent être proposés pour augmenter la sensibilité du diagnostic par RT-PCR. Selon les informations disponibles à ce jour, tous les cas confirmés du variant 20C/H655Y ont un lien épidémiologique direct ou indirect avec une commune des Côtes d’Armor et la diffusion du variant 20C/H655Y semble donc limitée actuellement à ce secteur géographique.
A cluster of infections by a 20C clade variant (“20C / H655Y variant”) was detected in a hospital in Côtes d’Armor, with cases occurring between January and March 2021. The particularity associated with the first confirmed cases of Infections with this variant is the possibility of presenting symptoms suggestive of COVID-19 with weakly positive or even negative RT-PCR on usual nasopharyngeal swabs. The virus is nevertheless detectable by the usual PCR techniques but seems to be found preferentially in the lower airways. To date, it has not been shown that this variant would be more transmissible or that it would lead to more severe forms, but its emergence is being investigated and the situation is being monitored in the territory via specific surveillance. In case of suspicion of infection with this variant (case definition and action to be taken, available on the website of Public Health France), samples beyond the nasopharyngeal sphere whenever possible should be proposed to increase the sensitivity of the diagnosis by RT-PCR. According to the information available to date, all the confirmed cases of the 20C / H655Y variant have a direct or indirect epidemiological link with a municipality in Côtes d’Armor and the spread of the 20C / H655Y variant therefore seems to be currently limited to this geographical area.
Public Health France has indicated that the Breton variant is limited to “a town in Côtes-d’Armor and the distribution of the 20C/H655Y variant therefore seems to be currently limited to this geographical area”. The geographical area is the city of Lannion.
Among the 13 confirmed cases, 11 come from the epidemic focus at the Lannion hospital center , another in the population (which is currently in strict confinement) and another in the Paris region, detected within the Pitié-Salpêtrière hospital.
Of these 13 confirmed cases, the ARS also confirms 7 deaths, including 5 contaminations with the Breton variant were detected by post-mortem samples. The remaining 6 are hospitalized. “Nothing indicates for the moment that this variant would be more contagious and more severe”, wishes to underline the ARS.
45,641 new cases of Covid-19 have been detected in France in the past 24 hours, according to figures released on Thursday. In total, 4,424,087 people have tested positive for Covid-19 in France.
The total number of people hospitalized in France with a positive Covid-19 diagnosis stands at 27,036, with 1,860 new admissions in 24 hours. 228 people have died in the past 24 hours in hospital. “The epidemic dynamic is strong” , underlined the Minister of Health Olivier Véran during a press conference Thursday.
“Professor Arnaud Fontanet, member of the scientific council, indicated Tuesday morning on on BFMTV that a ninth case of this Breton variant had been confirmed. According to our information, it could be a contamination spotted at the Pitié-Salpêtrière hospital in Paris, linked to the Lannion hospital center.”
Which territories are under surveillance?
In Brittany, five agglomerations are placed under surveillance (Morlaix, Lannion, Guingamp-Paimpol, Leff Armor and Saint-Brieuc). “In these areas, more extensive samples can be taken, in addition to the classic PCR, to try to identify this variant”, informs Stéphane Mulliez, director general of the Brittany regional health agency.
Will the measures announced be enough to curb the epidemic in France? We are already close to 100% saturation in intensive care. Whatever happens, we have two to three weeks before us before the measures taken have an effect on the intensive care admissions, during which the English variant will complete occupying the space.
Should we be afraid of the Breton mutant? It worries us as it is more difficult to detect by nasopharyngeal swab and can therefore go unnoticed. This makes the detection and isolation of patients difficult. Investigations are in progress by sequencing and by serology to estimate the extent of its diffusion. But it is too early to determine the magnitude and severity associated with it.
Interview with Epidemiologist Arnaud Fontanet, member of the French scientific council, in Le Journal de Dimanche
The coronavirus infection figures for the Covid-19 epidemic in Brittany this Friday show a sharply increasing incidence in the Côtes-d’Armor and Ille-et-Vilaine. Hospitalizations are also on the rise.
The incidence rate of Covid-19 cases in the region, that is to say the number of new cases diagnosed by PCR test during the last seven days, is on the rise, this Friday in Brittany. It stands at 145.2 cases per 100,000 inhabitants, an increase of 13.2% in two days. The positivity rate is 5.6%.
Ille-et-Vilaine retains the highest incidence rate, at 201.5 cases per 100,000 inhabitants (+21.1). Next are Côtes-d’Armor (156.2; +27.5), Morbihan (141; +5.5) and Finistère (74.3; +0.7).
A new variant (derived from Clade 20C) has been detected in the context of a cluster at the Lannion hospital center, in the Côtes d’Armor. …several patients presenting typical symptoms suggesting an infection by SARS-CoV-2 but a negative RT-PCR test result on nasopharyngeal samples and for whom the diagnosis could be made by serology or by performing RT-PCR on deep respiratory samples.
Where was the “Breton variant” discovered?
The alert was given after the Breton SARS-CoV-2 mutation was detected in a cluster that formed at the Lannion hospital center , in Côtes-d’Armor, in early March. Of the 79 cases of contamination, eight people were carriers of this variant. These eight people died. For now, there is nothing to link their death to the variant.
French Health Department Press Release – 15th March 2021 “Following the identification by sequencing, in Brittany, of a new variant (derived from Clade 20C), the health authorities put in place the necessary monitoring and support measures.”
French Health Department Annex 1 – 15th March 2021 “Definition of SARS-CoV-2 (COVID-19) infection and action to be taken concerning a new variant detected in Brittany (variant of clade 20C) “
French Health Department Annex 2 – 15th March 2021 “Population diagnostic strategy concerning a new variant of clade 20C detected in Brittany“
French Health Department Annex 3 – 15th March 2021 “Diagnostic strategy for active case finding in hospitals concerning a new variant of clade 20C detected in Brittany”
1- Identify cases in hospitals in connection with the cluster of new variant of the 20C clade detected in Brittany and to objectify the impact of circulation of the 20C clade variant in these establishments.
2- Identify the cases of infection by the new variant of clade 20C among the patients hospitalized on national territory who fall within the definition of case as defined in the document “Definition of cases of infection with SARS- CoV-2 (COVID-19) and what to do about a new variant detected in Brittany (variant of clade 20C) ”.
3- Explore the sites and the kinetics of viral excretion for the 20C variant
French authorities are investigating a new coronavirus variant, derived from clade 20C, found in the western Brittany region that is more difficult for tests to detect, though for now it does not appear to be more dangerous or contagious.
Stephane Mulliez, director of the regional ARS health service, said at a press conference Tuesday that a hospital biologist in Lannion, a city on the English Channel, sounded the alert after studying dozens of recent deaths.
Seven of the victims had shown classic coronavirus symptoms despite having negative PCR tests, which analyse nasal swabs and are usually highly accurate.
Further testing, of blood as well as mucus samples from deeper in the respiratory tract, confirmed the COVID diagnosis in the patients, who were all elderly and had underlying health risks, Mulliez said.
Update from Sortiraparis.com
“These cases have been confirmed after sequencing performed by Institut Pasteur that revealed “a new variant […] carrying nine mutations in the area coding for S protein, as well as in other viral regions”, the DGS stated in a message sent to health professionals.”
“We detected a novel strain descended from cluster 20C and defined by five mutations (ORF1a: I4205V, ORF1b:D1183Y, S: S13I;W152C;L452R)(Figure 1). This strain, CAL.20C, was first observed in July 2020 in 1/1230 samples from LA county and not detected in Southern California again until October. Since then, this strain’s prevalence has increased absolutely and relatively in Southern California, where by December it accounted for 24% of all samples (Figure 2A) and 36.4% (66/181) of our local Los Angeles cohort.”