New research published in the Centers for Disease Control and Prevention’s journal Emerging Infectious Diseases has confirmed the emergence of a new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant called HMN.19B from the viral clade 19B in France. The 19B viral clade — which includes the D614G variant — was prevalent in late 2019 but had since been rarely observed since early 2020 because of newer viral clades.
The variant is characterized by 18 amino acid mutations — including N501Y, L452R, and H655Y. There is evidence the variant can spread more rapidly than other SARS-CoV-2 strains.
The researchers write:
Whether HMN.19B will be less susceptible to protection by natural, therapeutic, or vaccine-induced immune responses remains to be determined. Several of its spike substitutions (N501Y, L452R, and H655Y) have been shown to require higher levels of neutralizing antibodies to be controlled, both in vitro and in vivo.”
Considering the limited data available on this new variant, the study authors emphasize an increased need for genomic surveillance and tracking.
Initial Detection of HMN.19B variant
Researchers were alerted to a new SARS-CoV-2 variant of interest on January 21, 2021, from PCR testing of an immunocompromised hospital staff member who presented with headache, fatigue, and rhinitis. Her partner in the same household and two nurses in close contact also tested positive for the variant. All four patients experienced mild symptoms and did not require hospitalization.
The hospital staff member and partner had a history of COVID-19 infection, but both had tested negative for SARS-CoV-2 protein N antibodies in January 2021. One of the nurses had received their first Pfizer-BioNTech vaccine dose 11 days before testing positive for the virus.
Genomic surveillance of the variant
Genomic sequencing showed four cluster members infected with a new variant related to clade 19B.
The variant contains 25 nucleotide substitutions, including 2 deletions and 8 amino acid substitutions on the SARS-CoV-2 spike protein.
Spread of the HMN.19B variant in Paris
Four weeks after, 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 staff worker working in the northeast area of Paris, three from the hematology department of a hospital, and eight unrelated cases on February 3-23 in different Paris hospitals.
Simultaneously, the National Reference Center for Respiratory Viral Infections in Lyon, France, detected 17 more people with closely related viruses to the HMN.19B variant. The related viruses contained more than seven similar spike protein mutations. Three people were from the greater Paris area, 10 from southeastern France, and 4 from southwestern France.