Genome‐based survey of the SARS‐CoV‐2 BF.7 variant from Asia

Abstract

The SARS-CoV-2 BF.7 variant represents one of the most recent subvariant under monitoring. At the beginning of the 2023 it caused several concerns especially in Asia because of a resurge in COVID-19 cases. Here we perform a genome-based integrative approach on SARS-CoV-2 BF.7 to shed light on this emerging lineage and produce some consideration on its real dangerousness. Both genetic and structural data suggest that this new variant currently does not show evidence of an high expansion capability. It is very common in Asia, but it appears less virulent than other Omicron variants as proved by its relatively low evolutionary rate (5.62 × 10 −4 subs/ sites/years). The last plateau has been reached around December 14, 2022 and then the genetic variability, and thus the viral population size, no longer increased. As already seen for several previous variants, the features that may be theoretically related to advantages are due to genetic drift that allows to the virus a constant adaptability to the host, but is not strictly connected to a fitness advantage. These results have further pointed that the genome-based monitoring must continue uninterruptedly to be prepared and well documented on the real situation.

Genetic and structural analyses reveal the low potential of the SARS‐CoV‐2 EG.5 variant

“…The phylogenomics of SARS‐CoV‐2 (available at https://gisaid.org/phylodynamics/global/nextstrain/), with a focus on global subsampling of the Omicron GISAID CLADE (Supporting Information: Figure ), reveals that the genomes of EG.5 (and its descendant EG.5.1) cluster within the GISAID CLADE 23 A (XBB.1.5). Although the sub‐lineage EG.5.1 constitute a clade labeled GISAID CLADE 23F, as recently shown in other emerging lineages, such as BF.7 in Asia 5 and XBB on global scale, 4 EG.5 and EG.5.1 are positioned within the main clade as an evolutionary blind background without any direct descendant, with a branch's length denoting the lack of a rapid diversification (see Supporting Information: Figure ).…”

“…8 The SARS-CoV-2 EG. 5 We also would like to thank all the authors who have kindly deposited and shared genomes on GISAID.…”

The effects of amino acid substitution of spike protein and genomic recombination on the evolution of SARS-CoV-2

“…Five major sublineages of Omicron, BA.1, BA.2, BA.3, BA.4, and BA.5, have been identified so far ( Tegally et al, 2022 ). Most recently, a series of novel Omicron subvariants have emerged, such as BA.2.75 ( Saito et al, 2022 ), BF.7 ( Scarpa et al, 2023a ), Deltacron ( Kreier, 2022 ), XE ( Rahimi and Bezmin Abadi, 2022b ), XF ( Chakraborty et al, 2022 ), BQ.1 ( Wang et al, 2022b ), BQ.1.1 ( Wang et al, 2022b ), XBB ( Imai et al, 2023 ), XBB.1 ( Arora et al, 2023 ), XBB.1.5 ( Tamura et al, 2022 ), XBB.1.16 ( Harris, 2023 ), and they have raised increasing concern. The timeline of emergence of variants is illustrated in Figure 2A .…”

“…BF.7 variant (also known as BA.5.2.1.7) is a derivative of BA.5 and has gained attention since the beginning of 2022, particularly in Asia ( Kelleni, 2023 ; Pan et al, 2023 ; Scarpa et al, 2023a ). Compared to BA.5, BF.7 carries an additional R346T mutation in the RBD and shares an identical N-terminal domain (NTD) ( Scarpa et al, 2023a ).…”

“…BF.7 variant (also known as BA.5.2.1.7) is a derivative of BA.5 and has gained attention since the beginning of 2022, particularly in Asia ( Kelleni, 2023 ; Pan et al, 2023 ; Scarpa et al, 2023a ). Compared to BA.5, BF.7 carries an additional R346T mutation in the RBD and shares an identical N-terminal domain (NTD) ( Scarpa et al, 2023a ). The R346T mutation has been associated with enhancing the virus’s ability to evade neutralizing antibodies generated by vaccines or previous infection ( Akif et al, 2023 ).…”