Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant

In late 2022, various Omicron subvariants emerged and cocirculated worldwide. These variants convergently acquired amino acid substitutions at critical residues in the spike protein, including residues R346, K444, L452, N460, and F486. Here, we characterize the convergent evolution of Omicron subvariants and the properties of one recent lineage of concern, BQ.1.1. Our phylogenetic analysis suggests that these five substitutions are recurrently acquired, particularly in younger Omicron lineages. Epidemic dynamics modelling suggests that the five substitutions increase viral fitness, and a large proportion of the fitness variation within Omicron lineages can be explained by these substitutions. Compared to BA.5, BQ.1.1 evades breakthrough BA.2 and BA.5 infection sera more efficiently, as demonstrated by neutralization assays. The pathogenicity of BQ.1.1 in hamsters is lower than that of BA.5. Our multiscale investigations illuminate the evolutionary rules governing the convergent evolution for known Omicron lineages as of 2022

Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants

In late 2022, SARS-CoV-2 Omicron subvariants have become highly diversified, and XBB is spreading rapidly around the world. Our phylogenetic analyses suggested that XBB emerged through the recombination of two cocirculating BA.2 lineages, BJ.1 and BM.1.1.1 (a progeny of BA.2.75), during the summer of 2022. XBB.1 is the variant most profoundly resistant to BA.2/5 breakthrough infection sera to date and is more fusogenic than BA.2.75. The recombination breakpoint is located in the receptor-binding domain of spike, and each region of the recombinant spike confers immune evasion and increases fusogenicity. We further provide the structural basis for the interaction between XBB.1 spike and human ACE2. Finally, the intrinsic pathogenicity of XBB.1 in male hamsters is comparable to or even lower than that of BA.2.75. Our multiscale investigation provides evidence suggesting that XBB is the first observed SARS-CoV-2 variant to increase its fitness through recombination rather than substitutions

Evaluation of major nutrients regulating the growth of diatoms in Harima-Nada, the Seto Inland Sea, Japan

　In the eastern Seto Inland Sea, dissolved inorganic nitrogen has decreased due to the reduction of nutrient inputs, and there have been changes in the total cell density and the composition of the phytoplankton assemblages. The major phytoplankton component was diatoms, and the contribution was always over 90 percent of total phytoplankton since the 1990s. In order to elucidate growth characteristics and nutrient consumption of diatom species, we conducted major nutrients-enrichment bottle incubation experiments on shipboard using the surface waters in Harima-Nada, eastern part of the Seto Inland Sea. Seawater incubation experiments demonstrated that nutrient environments for phytoplankton are in a state of nitrogen-limitation in Harima-Nada. The addition of nitrate to surface waters of this coastal region promotes blooms of large chain-forming diatom species. These results suggest that diatom blooms cause depletion of the nutrients (mainly nitrogen) in Harima-Nada