Emergence of the SARS‐CoV‐2 B.1.1.7 variant observed at the Poitiers University Hospital

To The Editor,

Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is responsible for the highly spreading coronavirus disease 2019 (COVID‐19). Currently (May 11, 2021), the total number of confirmed COVID‐19 cases has reached more than 159 million, with nearly 3.3 million deaths worldwide. ¹ Recently, a new variant of SARS‐CoV‐2 named B.1.1.7, defined by multiple spike protein changes, including the N501Y mutation, started to spread in the United Kingdom. ² The first reported case was retrospectively identified on September 20, 2020, in the London area. During the third week of December (from the 14th to the 20th), it already represented half of the total SARS‐CoV‐2 strains sequenced in the UK. Two weeks later, from December 28, it reached more than 70%. ³ The amino acid change N501Y has been suggested as increasing the binding affinity of the virus to its receptor, the human ACE2. ⁴ Davies et al. ⁵ estimated that the B.1.1.7 variant is 56% more transmissible (95% confidence interval [CI] 50%–74%) than previously identified SARS‐CoV‐2 variants. In addition, the same authors showed that B.1.1.7 infection was associated with 55% (95% CI 39%–72%) higher mortality. ⁶ Concomitantly with the emergence of the B.1.1.7 variant, the UK experienced a new epidemic peak, with up to 50,000 new cases of SARS‐CoV‐2 infections per day at the beginning of January 2021. The number of deaths linked to COVID‐19 has also increased, with an average of 1300 deaths per day at the end of January. ⁷

The laboratory of virology of the Poitiers University Hospital performs polymerase chain reaction (PCR) screening for SARS‐CoV‐2 for in‐ and out‐patient from all the departments in the northern part of the New Aquitaine region located in the southwest of France, which represents an area of 25,809 km² for a population of 1.78 million people. PCR tests are carried out from nasopharyngeal samples using the Thermo Fisher Scientific TaqPath™ COVID‐19 reverse‐transcription polymerase chain reaction (RT‐PCR) Kit. Interestingly, the nucleotide deletion 69–70 in the spike protein, present in variant B.1.1.7, results in nondetection of the S gene using this RT‐PCR assay. ⁸ Epidemiological surveillance of the B.1.1.7 variant in our laboratory began on December 14, 2020, by monitoring strains with undetected S gene while N and ORFa/b genes were detected with Ct values less than 29. From February 10, 2021, detection of the N501Y mutation by RT‐PCR (VIRSNIP SARS‐COV‐2 N501Y, Tib Molbiol) was carried out additionally on all positive samples. Lack of detection of the S gene using the Thermo Fisher Scientific assay associated with the presence of the N501Y mutation was strongly suggestive of a B.1.1.7 variant. Sequencing of the receptor‐binding domain of the spike protein on several strains confirmed the presence of the B.1.1.7 variant among the evocative profiles, validating the adopted strategy.

From December 14, 2020 to March 07, 2021, 163,880 SARS‐CoV‐2 PCR screening tests were performed; 9612 (5.8%) were positive and 1353 (28.8%) of the positive results displayed suspect profiles for B.1.1.7 variant. Figure 1 shows the proportion of the B.1.1.7 variant among the total number of SARS‐CoV‐2 cases detected per week. During the week of December 21–27, B.1.1.7 profile represented only 1% of positive SARS‐CoV‐2 PCR tests. From the week of January 11, however, this percentage soared from 9% to as high as 76%, during the week of March 3. Moreover, according to the data published by Public Health France on epidemiological surveillance in the Vienne Department, ⁹ a similar climb in the number of hospitalizations for COVID‐19 was observed (Figure 2). However, it is interesting to note that, at the same time, the number of intensive care admissions remained stable. We observed that over this period, the age distribution of SARS‐CoV‐2 infections was modified by the emergence of the B.1.1.7 variant; the 25–45‐year‐old age group was most affected by B.1.1.7 SARS‐CoV‐2, whereas non‐B.1.1.7 SARS‐CoV‐2 remained predominant among patients over 65. In the 0–4‐year‐old age group, B.1.1.7 variant represented 50% of the cases, while it corresponded to only 20% in those over 65. These data were not, or very little, influenced by the vaccination, which was still beginning since only 4% of the population were vaccinated (one and two doses) on March 7. They suggest a more marked tropism of the B.1.1.7 variant for the younger age groups.

Figure 1.

Proportion of SARS‐CoV‐2 B.1.1.7 variant profile per week, and the total number of SARS‐CoV‐2 cases detected per week at Poitiers University Hospital. SARS‐CoV‐2, severe acute respiratory syndrome coronavirus 2

Figure 2.

Evolution of the number of newly hospitalized patients in Vienne Department per week linked to SARS‐CoV‐2 in conventional or in intensive care hospitalizations compared to the overall emergence curve of B.1.1.7 variant (proportion of B.1.1.7 variant on the all SARS‐CoV‐2 detected). SARS‐CoV‐2, severe acute respiratory syndrome coronavirus 2

In conclusion, our results show that in less than 4 months, the B.1.1.7 variant became the majority variant in a region where it had not previously circulated. Its emergence has been correlated with an increase in the number of positive cases already reported in the regions previously affected by this variant, particularly in the youngest age groups, which up until then had not been affected by COVID‐19. ¹⁰ The consequences on the number of hospitalized patients are not yet certain, particularly regarding hospitalizations in intensive care, but they will need to be closely monitored over the weeks to come. Likewise, the impact of vaccination deployment on the evolution of the circulation of this highly contagious variant will constitute a valuable predictive indicator of the evolution of the pandemic over the months to come.

CONFLICT OF INTERESTS

All the authors declare that there are no conflict of interests.

AUTHOR CONTRIBUTIONS

Florent Hubert and Nicolas Leveque wrote the draft. Laurence Boinot and Ursula Noury provided the epidemiological data necessary for the interpretation of the virological results. Céline Chessa, Agnès Beby‐Defaux, Anne Bourgoin, Andy Lariviere, Mohammed Benlaassri, and Magali Garcia performed virological tests and contributed to the revision of the manuscript. All authors approved the final version of the manuscript.