We report a cluster of two sequences characterized by a unique array of 18 mutations, including new non-synonymous changes in the same critical spike amino acid positions, E484Q and N501T. This lineage seems to have emerged independently from the nationally widespread B.1.1.28, as previously reported for P.1 and P.2, and adds up to the composition of a complex epidemiological scenario of the SARS-CoV-2 pandemic in Brazil.
Our analysis revealed the circulation of a putative new variant derived from lineage B.1.1.28, and represented by two genome sequences in our dataset, LBI215 (complete, 99.81% 10x genome coverage, 98.07% 100x genome coverage, average sequencing depth: 1532x, pangolin original classification: B.1.235) and LBI218 (partial, 76.20% 10x genome coverage, 57.45% 100x genome coverage, average sequencing depth: 595x, pangolin original classification: B.1.1.94). These two sequences form a well-supported (SH-aLRT = 100) monophyletic clade characterized by a unique set of 18 nucleotide mutations.
Beyond harboring multiple exclusive synonymous (C1627U, A10888G, C12664U, C24904U, C27807U, A28271U) and non-synonymous (G5180A: ORF1ab D1639N, G9929A: ORF1ab D3222N, G23012C: Spike E484Q, A23064C: Spike N501T, C24374U: Spike L938F, G24410A: Spike D950N, C28311U: Nucleocapsid P13L) SNPs, this lineage also possesses mutations present in other VOCs: deletion 11288-11296 (ORF1ab 3675-3677 SGF; shared by P.1, B.1.1.7 and B.1.351), C21614U (Spike L18F, P.1) and C28253U (Synonymous, P.2). Two additional deletions are present in these sequences: deletions 28881-28889 (Nucleocapsid 203-206 RGTS(T)) and 29581, which causes a frameshift mutation in ORF10. Additional mutations covered only in the LBI215 genome include: G3617A, ORF1ab V1118I; C21846T, spike T95I; deletion 21986-21991, Spike 142/143 GV; T23542C, synonymous. To ascertain that these mutations were not assembly artifacts, we confirmed their presence in the raw sequencing data .
Virological.org preprint : Increasing frequency of SARS-CoV-2 lineages B.1.1.7, P.1 and P.2 and identification of a novel lineage harboring E484Q and N501T spike mutations in Minas Gerais, Southeast Brazil
Original press story: UFMG scientists announce they have discovered a new variant of the coronavirus