New research published in the journal Centers for Disease Control and Prevention Emerging infectious diseases has confirmed the onset of a new variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) called HMN.19B of viral clade 19B in France. Viral clade 19B, which includes variant D614G, was common in late 2019, but has since been rarely observed since early 2020 due to newer viral clades.
The variant is characterized by 18 amino acid mutations, including N501Y, L452R, and H655Y. There is evidence that the variant can spread more rapidly than other SARS-CoV-2 strains.
It remains to be determined whether HMN.19B will be less susceptible to protection from natural, therapeutic, or vaccine-induced immune responses. Several of its spike replacements (N501Y, L452R, and H655Y) have been shown to require higher levels of neutralizing antibodies to control, in vitro and in vivo. “
Given the limited data available on this new variant, the study authors emphasize the growing need for genomic surveillance and monitoring.
Initial detection of variant HMN.19B
Investigators were alerted to a new SARS-CoV-2 variant of interest on January 21, 2021, based on PCR tests of an immunocompromised hospital staff member who presented with headache, fatigue and rhinitis. Her partner from the same home and two nurses in close contact also tested positive for the variant. All four patients experienced mild symptoms and did not need hospitalization.
The hospital staff member and staff member had a history of COVID-19 infection, but both had tested negative for antibodies to SARS-CoV-2 protein N in January 2021. One of the nurses had received the first dose of Pfizer-BioNTech vaccine 11 days before testing positive for the virus.
Genomic surveillance of the variant
Genomic sequencing showed four members of the cluster infected with a new variant related to clade 19B.
The variant contains 25 nucleotide substitutions, including 2 deletions and 8 amino acid substitutions in SARS-CoV-2 ear protein.
Dissemination of variant HMN.19B in Paris
Four weeks later, the researchers identified the HMN.19B variant in the genomic sequencing of 12 people living in Paris who tested positive for COVID-19 infection. This included a prison worker working in the north-east of Paris, three from a hospital’s hematology department and eight unrelated cases between 3 and 23 February at various hospitals in Paris.
Simultaneously, the National Reference Center for Respiratory Viral Infections in Lyon, France, detected 17 more people with viruses closely related to the HMN.19B variant. Related viruses contained more than seven similar spike protein mutations. Three people were from the Paris area, 10 from the south-east of France and 4 from the south-west of France.