bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2023.07.23.549423

Phylogeny and evolution of the SARS-CoV-2 spike gene from December 2022 to February 2023

Kao, H.-W.
View original source ↗Export metadata ↓

Abstract

BackgroundBy the end of 2022, new variants of SARS-CoV-2, such as BQ.1.1.10, BA.4.6.3, XBB, and CH.1.1, emerged with higher fitness than BA.5. MethodsThe file (spikeprot0304), which contains spike protein sequences, isolates collected before March, 4, 2023, was downloaded from Global Initiative on Sharing All Influenza Data (GISAID). A total of 188 different spike protein sequences were chosen, of which their isolates were collected from December 2022 to February 2023. These sequences did not contain undetermined amino acid X, and each spike protein sequence had at least 100 identical isolate sequences in GISAID. Phylogenetic trees were reconstructed using IQ-TREE and MrBayes softwares. A median-join network was reconstructed using PopART software. Selection analyses were conducted using site model of PAML software. ResultsThe phylogenetic tree of the spike DNA sequences revealed that the majority of variants belonged to three major lineages: BA.2 (BA.1.1.529.2), BA.5 (BA.1.1.529.5), and XBB. The median network showed that these lineages had at least six major diversifying centers. The spike DNA sequences of these diversifying centers had the representative accession IDs (EPI_ISL_) of 16040256 (BN.1.2), 15970311 (BA.5), 16028739 (BA.5.11), 16028774 (BQ.1), 16027638 (BQ.1.1.23), and 16044705 (XBB.1.5). Selection analyses revealed 26 amino-acid sites under positive selection. These sites included L5, V83, W152, G181, N185, V213, H245, Y248, D253, S255, S256, G257, R346, R408, K444, V445, G446, N450, L452, N460, F486, Q613, Q675, T883, P1162, and V1264. ConclusionThe spike proteins of SARS-CoV-2 from December 2022 to February 2023 were characterized by a swarm of variants that were evolved from three major lineages: BA.2 (BA.1.1.529.2), BA.5 (BA.1.1.529.5), and XBB. These lineages had at least six diversifying centers. Selection analysis identified 26 amino acid sites were under positive selection. Continued surveillance and research are necessary to monitor the evolution and potential impact of these variants on public health.

Explore related subjects

evolutionary biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Kao, H.-W.. 2023-07-24. Phylogeny and evolution of the SARS-CoV-2 spike gene from December 2022 to February 2023. https://doi.org/10.1101/2023.07.23.549423

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Isoform inflation and annotation heterogeneity can confound Kunitz-repertoire comparisons in blood-feeding animals: a gene-level reappraisal

Hematophagy has arisen independently many times across Metazoa, and recurrent anticoagulant protein families in blood-feeders are often read as convergent recruitment - the Kunitz/BPTI domain a paradigm case, with the leech an oft-cited low-Kunitz exception. We re-examine this at the gene level and ask whether a confirmatory cross-phylum test of this blood-feeding/anticoagulant association is feasible with public genomes. Applying an auditable gene-level protocol (one longest-isoform representative per gene; conservation-checked protein to gene mapping) to eight metazoan lineages, we find no consistent, universal elevation of whole-genome gene-level Kunitz-repertoire size in these blood-feeders (blood-feeder median 18 genes vs non-blood-feeder median 39; a descriptive comparison of non-independent taxa, not a formal test). Protein-entry counts inflate gene-level Kunitz counts by up to ~4.6x (mosquito 23 to 5), and neither this inflation nor proteome-wide isoform density (1.0-2.7x) tracks diet, so protein-entry comparisons are an unreliable basis for repertoire claims. Separately, deterministic bookkeeping under a fixed topology and a no-reversal rule counts 12 independent blood-feeding origins (11 if the ancestral lamprey is treated as parasitic with two losses); a non-exhaustive screen of annotated public genomes yielded only one candidate blood/non-blood pair (bedbug), and, under the pre-registered simulation scenario, only a cross-origin heterogeneity endpoint is attainable within a realistic origin ceiling, and only under strong heterogeneity (among-origin SD >= 3-4). An exploratory, feasibility-grade secretome-composition estimate did not meet the pre-registered criterion. We offer a gene-level, annotation-aware re-analysis, a caution about isoform/annotation bias in cross-phylum comparisons, and an account of what current data can and cannot support.

evolutionary biology↗
bioRxiv2026

Denisovan introgression left differential selection regimes in Humans and Neanderthals on the SLC30A9 gene

Signals of positive selection around the SLC30A9 gene have been reported in human populations outside Africa. Selection likely acted on a highly differentiated single-nucleotide polymorphism, rs1047626, leading to a non-synonymous substitution in the encoded zinc transporter. Because of the striking similarity between the putatively selected SLC30A9 haplotype observed in several current human populations and the Denisovan individual, previous work has proposed adaptive introgression. Yet alternative explanations, including ancient human variation, and the precise archaic source -Neanderthal or Denisovan- remained unresolved. Considering the potentially complex evolution of SLC30A9, we applied Approximate Bayesian Computation (ABC) algorithms coupled to machine learning to investigate the most plausible evolutionary origin of this substitution. After modelling different evolutionary scenarios with forward-in-time simulations, our results highlight that the most probable scenario is a Denisovan origin of the rs1047626 polymorphism. However, the allele likely introgressed into Neanderthals first and was then passed into non-African modern humans. Moreover, the derived allele frequency for rs1047626 across several African populations is consistent with back-to-Africa migrations. Finally, our ABC analyses indicate strong positive selection in East Asian populations and other out-of-Africa populations, whereas in Neanderthal populations, the selection coefficient was probably neutral or slightly deleterious.

evolutionary biology↗
bioRxiv2026

Distinct associative learning abilities for colour and odour in the flower-feeding Drosophila elegans and the fruit-feeding Drosophila melanogaster

Animal behaviour is both innately constrained and shaped by learning. This mosaic organization has evolved in response to species-specific ecological demands and may differ between sensory modalities. Flower-visiting animals are a particularly useful system for investigating the relationship between sensory ecology and learning because they rely on multiple floral cues, particularly odour and colour, to locate food sources. However, it remains largely unexplored whether specialization on floral resources entails divergence in learning abilities across sensory modalities. Drosophila elegans is a flower-feeding species that depends heavily on floral resources throughout its life; adults spend much of their time on flowers and larvae develop on fallen flower leaves. Here, we compared odour-reward and colour-reward associative learning between the flower-feeding D. elegans and the fruit-feeding D. melanogaster. We found that, under conditions of equilibrated motivation, odour- and colour-preference, and using the same sugar reward, D. elegans exhibited poorer odour-reward learning performance but better colour-reward learning performance than D. melanogaster. These results suggest that the modality-specific eligibility of sensory information to enter into associations, known as the 'Garcia-effect' in experimental psychology, can evolve oppositely between species. This highlights the relationship between ecological specialization and mnemonic processing, and shows that biological 'intelligence' is not general.

evolutionary biology↗