Biology subjects

Geng, R.

Publications and source records attributed to Geng, R..

15 recordsLinked to original sources

bioRxiv2026

KDM4 inhibition alters H3K9me3 distribution and developmental responses in SETDB1-deficient embryonic stem cells

SETDB1 contributes to histone H3 lysine 9 methylation, whereas KDM4 demethylases act on H3K9 and, for KDM4A-C, H3K36. We examined whether Setdb1 status modifies responses to the KDM4-family inhibitor QC6352 in embryonic stem cells (ESCs) and embryoid bodies (EBs). QC6352 shifted Setdb1-depleted ESC colonies toward more compact morphology and increased alkaline-phosphatase (AP) staining, but also affected Setdb1-intact cells. Separate Kdm4a, Kdm4b, and Kdm4c knockdowns identified overlapping and member-specific transcriptional responses. Factorial RNA-seq revealed broadly concordant transcriptional responses to KDM4 inhibition in Setdb1-intact and depleted ESCs, alongside a smaller subset of genes with genotype-dependent treatment effects. Within this subset, two gene modules showed attenuation or reversal of Setdb1-associated expression changes following KDM4 inhibition. ChIP-seq revealed changes in the relative distribution of H3K9me3, H3K36me3, and H3K4me3 between promoters and gene bodies following KDM4 inhibition. KDM4 inhibition altered H3K9me3 distributions across repeat families in both Setdb1-intact and depleted ESCs. QC6352 also altered EB morphology and produced transcriptional responses that differed between ESCs and EBs. These findings show that KDM4 inhibition remodels chromatin and transcription in both Setdb1-intact and depleted ESCs, with Setdb1 status influencing a subset of transcriptional responses.

molecular biology↗

bioRxiv2026

Early-onset spontaneous murine mammary tumors show increased lymphocyte representation and reduced MHC antigen presentation

Simple Summary Not all breast tumors behave the same way, and part of the reason may be inherited rather than caused by the tumor itself. Using mice that carry the same cancer-causing HER2/neu gene but differ in genetic background, we found that introduction of the PWK/PhJ genetic background was associated with tumors that appeared about a month earlier. These early tumors contained a larger proportion of immune cells, including T and B cells, but the T-cell population showed reduced expression of genes associated with cytotoxic activity. At the same time, the tumors had lower levels of proteins and genes that let the immune system recognize tumor cells, alongside higher levels of structural proteins that can make tissue stiffer and easier for cancer to invade. These findings suggest that genetic background shapes not only how quickly breast tumors arise but also how well the immune system can recognize them, a distinction that may matter for future immune-based treatments. Background/Objectives: Genetic background modifies cancer risk and phenotype in humans, but its influence on the tumor immune microenvironment and antigen-presentation machinery in ErbB2 (HER2/neu)-driven breast cancer is not well defined. We used a genetically diverse mouse cross to test whether the wild-derived PWK/PhJ background alters immune representation and antigen presentation in a NeuT model of HER2/neu-positive breast cancer. Methods: Previously, quantitative trait locus (QTL) mapping using Diversity Outbred mice and r/qtl2 identified candidate loci driving tumor onset and growth. The wild-derived PWK/PhJ genetic background was predicted to harbor genes that regulated early onset of HER2/neu-driven tumors. BALB NeuT and (BALBxPWK) F1 NeuT female mice were monitored twice weekly for spontaneous mammary tumor onset and growth. Tumor immune composition was profiled by single-cell RNA sequencing. Protein abundance was measured by data-independent acquisition proteomics in formalin-fixed, paraffin-embedded tumor tissue (n=5 per genotype). Single-nucleus multiome (RNA + ATAC), bulk RNA-seq, and H3K27ac datasets from the same strain comparison were analyzed for focused MHC II cross-layer analyses. Results: As predicted, (BALBxPWK) F1 NeuT mice developed tumors significantly earlier than the parental BALB NeuT mice (10 vs. 15 weeks of age; p < 0.0001). In the scRNA-seq dataset, F1 tumors showed greater representation of Cd3e-expressing T cells and a Cd79a-expressing B-cell population not detected in BALB NeuT tumors, and a distinct neutrophil cluster; F1 T cells also showed lower expression of the cytotoxicity-associated genes Tox, Ltk, Nkg7, and Gzmb relative to BALB NeuT tumor-infiltrating T cells. Proteomics identified 46 differentially abundant proteins (25 higher, 21 lower in F1), with coordinate down-regulation of Stat1, Tapbp, Parp9, and Dtx3l alongside MHC class I and II proteins and up-regulation of extracellular-matrix and elastic-fiber proteins. Focused cross-layer analysis showed lower whole-tumor expression of a Stat1/MHC II-associated gene set together with reduced epithelial chromatin accessibility at selected regions near Cd74 and H2-Aa. Conclusions: The PWK/PhJ genetic background is associated with earlier HER2-driven tumor onset, greater lymphocyte proportion, and reduced activity of a STAT1-associated antigen-presentation program despite similar post-onset tumor growth kinetics.

cancer biology↗

bioRxiv2026

PWK genetic background reprograms heterochromatin and malignant epithelial states in Neu-driven mammary tumors

Genetic background can alter the latency and behavior of cancers initiated by the same oncogenic driver, but how inherited variation reshapes the regulatory landscape that permits tumor development remains poorly understood. The PWK genetic background accelerates mammary tumor onset in the NeuT model. We compared PWK NeuT and BALB NeuT tumors using tumor-level RNA-seq, histone ChIP-seq, and single-cell multiome profiling. PWK tumors exhibited broad transcriptional reprogramming characterized by reduced immune-associated expression and increased epithelial differentiation and neuronal-like programs. Chromatin remodeling was spatially redistributed rather than uniformly increased or decreased. PWK tumors showed expansion of H3K9me3- and H4K20me3-associated chromatin, while both marks were depleted across many expressed genes and concentrated within selected intergenic and repeat-rich territories, revealing coordinated redistribution of constitutive heterochromatin. Single-cell multiome profiling showed that broad epithelial representation remained similar between strains, yet specific malignant states were strongly strain biased. Integrated RNA and accessibility analyses identified concordant strain-selective regulatory programs and candidate loci, while trajectory analysis revealed distinct epithelial state transitions between PWK NeuT and BALB NeuT tumors. Together, these findings indicate that inherited genetic background reshapes transcriptional programs, heterochromatin organization, and malignant epithelial state trajectories in NeuT mammary tumors, providing a regulatory framework for understanding strain-dependent differences in tumor onset.

cancer biology↗

bioRxiv2025

The role of climatic anomalies in agricultural instability and settlement abandonment in northeastern Germany during the Migration Period

The Late Antique Migration Period (LAMP; 300-700 CE) in northeastern Germany was marked by significant socio-environmental transformations, including the decline of human activity, settlement abandonment, and a reduction in cereal cultivation, particularly rye (Secale cereale). While these changes are well-documented in pollen and archaeological records, their underlying drivers--whether socio-political instability, agricultural crises, or environmental pressures--remain debated. Here, we synthesize multiproxy evidence, including high-resolution pollen data, climate reconstructions, and archaeobotanical data to explore the interplay between climatic fluctuations, agricultural practices, and human mobility during LAMP. Although previous studies have examined socio-environmental changes during the Migration Period using archaeological and palynological evidence, this study is the first to integrate high-resolution pollen records, archaeobotanical data, and climate model simulations specific to northeastern Germany to systematically evaluate the role of climatic anomalies in shaping agricultural and demographic patterns. We focus on the Dark Age Cold Period (DACP; 350-700 CE) and the Late Antique Little Ice Age (LALIA; 536-660 CE), which brought cold and wet conditions to northern Europe, likely disrupting agricultural productivity and fostering the spread of Claviceps purpurea (ergot), a toxic fungus affecting cereal crops, particularly rye. Our findings suggest that these climatic anomalies created favorable conditions for ergot outbreaks, leading to agricultural instability and reduced food security. This, combined with socio-political pressures, may have contributed to the observed decline in human activity and settlement abandonment. By integrating palynological, climatic, and archaeobotanical data, this study highlights the complex interactions between environmental stressors and human responses during the LAMP. We suggest that the climatic anomalies of the DACP and LALIA, coupled with the vulnerability of cereal crops to ergot infestation, influenced agricultural and demographic shifts in northeastern Germany. This review not only refines our understanding of the DACP and the LALIA but also demonstrates how climatic stressors and natural hazards can amplify socio-political vulnerabilities in past societies (or pre-industrial societies).

ecology↗

bioRxiv2025

Stable Maintenance of Two-Cell-Like Cells from Embryonic Stem Cells Reveals Chromatin and Super Enhancer Regulation of MERVL Elements

Mouse embryonic stem cells (ESCs) occasionally transit into a rare two-cell-like (2C) state characterized by transient activation of endogenous retroviruses such as MERVL and expression of 2C-specific genes including the Zscan4 cluster. These 2C-like cells (2CLCs) resemble early blastomeres and display expanded developmental potential, but their unstable and sporadic nature has hindered mechanistic studies. Here, we establish stable 2CLCs (s2CLCs) that maintain persistent MERVL expression and homogeneous 2C gene activation. Live-cell imaging revealed uniform and sustained MERVL activity in s2CLCs, contrasting with the heterogeneous and transient expression observed in conventional ESCs. Transcriptome profiling demonstrated robust induction of 2C-specific regulatory networks, and embryoid body differentiation combined with machine learning uncovered increased lineage variability and expanded developmental trajectories. Epigenomic profiling further revealed unique chromatin states, distinctive super enhancer landscapes, and active enhancer marking at MERVL loci. Together, these findings demonstrate that stable maintenance of the 2C-like state is achievable in vitro, providing a powerful model to dissect ERV-driven transcriptional regulation, epigenomic remodeling, and totipotent-like developmental potential.

developmental biology↗

bioRxiv2025

Automated Image-Based Profiling of Pluripotent Stem Cell Colonies

Quantitative image analysis is essential for advancing stem cell biology, developmental studies, and drug discovery, yet most workflows still rely on manual or semi-quantitative scoring that is slow, subjective, and poorly scalable. A major challenge is converting complex colony morphologies into reproducible, high-dimensional datasets. To address this gap, we developed ColonyQuant, an open-source platform that integrates automated colony segmentation, alkaline phosphatase (AP) intensity quantification, morphometric profiling, and statistical classification into a single workflow. ColonyQuant computes per-colony functional readouts alongside comprehensive shape descriptors, capturing both staining intensity and structural features in a unified framework. Applied to embryonic stem cells (ESCs) treated with a selective KDM4 histone-demethylase inhibitor, ColonyQuant revealed dose-dependent reductions in colony area and integrated AP signal, together with systematic remodeling of morphometric metrics. Multivariate analyses robustly stratified treatment groups and identified intensity and solidity as principal features capturing dose-dependent colony responses. By transforming subjective scoring into objective, scalable, and biologically interpretable phenotyping, ColonyQuant provides a reproducible platform for stem cell research and high-content screening.

developmental biology↗

bioRxiv2024

Equip Fusobacterium nucleatum genetic tool kits with compatible shuttle vectors and engineered intermediatory E. coli strains for enhanced transformation efficiency

Fusobacterium nucleatum, an oral microbe, is implicated in various human diseases, including oral-related diseases and tumors. However, efficient transformation was only achieved in limited strains of this bacterium. The challenges in conducting molecular level investigations of most strains due to their genetic intractability have hindered the biological studies of F. nucleatum. The restriction-modification (RM) systems is one of the known obstacles for efficient DNA transformation. Here, we used single molecule real time sequencing to elucidate the RM recognition sites and the corresponding methyltransferases (MTases) in two F. nucleatum strains. Based on the identified MTases, we engineered intermediatory E. coli host strains to bypass the RM systems, and showed that the plasmids harbored by these intermediatory strains can be efficiently electro-transformed, reaching 5000 transformants per microgram plasmids, paving the way for the development of efficient genetic modification tools. Furthermore, we successfully demonstrated that the conjugation-based DNA delivery to F. nucleatum can bypass the requirement of MTase methylations. By exploring the native plasmids from F. nucleatum, we identified new backbones for construction of shuttle vectors and established a dual-plasmid system for the first time, offering new avenues for genetic manipulation in this bacterium. Additionally, we evaluate promoters with variable strengths with a luciferase-based reporter system in F. nucleatum, providing valuable insights for future gene editing studies in bacterium and contributing to our understanding of its pathogenesis. All the tools developed in this study was shared via the WeKwikgene (https://wekwikgene.wllsb.edu.cn/). Impact StatementFusobacterium nucleatum, a key opportunistic pathogen implicated in periodontal diseases, rheumatoid arthritis, and tumors, presents significant challenges due to its limited transformation efficiency and lack of gene-editing tools. In this study, we present an advancement -a streamlined and robust pipeline that enhances transformation efficiency by approximately 103-fold in F. nucleatum, reaching 5000 CFU per microgram plasmids. This represents a significant breakthrough, marking the first report to achieve such a remarkable improvement in transformation efficiency in this pathogen. This improvement paves the way for the genome-wide level mutagenesis study in this bacterium.

microbiology↗

bioRxiv2024

Unconventional IFNω-like genes dominate the type I IFN locus and the constitutive antiviral responses in bats

Bats are the natural reservoir hosts of some viruses, some of which may spillover to humans and cause global-scale pandemics. Different to humans, bats may coexist with high pathogenic viruses without showing symptoms of diseases. As one of the most important first defenses, bat type I interferon (IFN-Is) were thought to play a role during this virus coexistence and thus were studied in recent years. However, there are arguments that whether bats have a contracted genome locus or constitutive expressed IFNs, mainly due to species-specific findings. We hypothesized that because of the lacking of pan-bat analysis, the common characters for bat IFN-Is have not been revealed yet. Here, we characterized the IFN-I locus for 9 Yangochiroptera bats and 3 Yinpterochiroptera based on the their high quality bat genomes. We also compared the basal expression for 6 bats and compared the antiviral, anti-proliferative activity and thermo-stability of a representative Rhinolophus bat IFNs. We found a dominance of unconventional IFN{omega}-like responses in the IFN-I system, which is unique to bats. In contrast to IFNa-dominated IFN-I loci in the majority of other mammals, bats generally have shorter IFN-I loci with more unconventional IFN{omega}-like genes (IFN{omega} or related IFNa{omega}), but with less or even no IFNa genes. In addition, bats generally have constitutively expressed IFNs, the highest expressed of which is more likely an IFN{omega}-like gene. Likewise, the highly expressed IFN{omega}-like protein also demonstrated the best antiviral activity, anti-proliferative activity or thermo-stability, as shown in a representative Rhinolophus bat species. Overall, we revealed pan-bat unique characteristics in IFN-I system, which provide insights into our understanding of the innate immunity that contribute to a special coexistence between bats and viruses.

immunology↗

bioRxiv2023

PNLDC1 catalysis and postnatal germline function are required for piRNA trimming, LINE1 silencing, and spermatogenesis in mice

PIWI-interacting RNAs (piRNAs) play critical and conserved roles in transposon silencing and gene regulation in the animal germline. Two distinct piRNA populations are present during mouse spermatogenesis: pre-pachytene piRNAs in fetal/neonatal testes and pachytene piRNAs in adult testes. PNLDC1 is required for both pre-pachytene piRNA and pachytene piRNA 3 end maturation in multiple species. However, whether PNLDC1 is the bona fide piRNA trimmer and the physiological role of 3 trimming of two distinct piRNA populations in spermatogenesis remain unclear. Here, by inactivating Pnldc1 exonuclease activity in vitro and in mice, we reveal that PNLDC1 trimmer activity is required for both pre-pachytene piRNA and pachytene piRNA 3 end trimming and male fertility. Furthermore, conditional inactivation of Pnldc1 in postnatal germ cells causes LINE1 transposon de-repression and spermatogenic arrest in mice. This indicates that pachytene piRNA trimming, but not pre-pachytene piRNA trimming, is essential for mouse germ cell development and transposon silencing. Our findings highlight the potential of inhibiting germline piRNA trimmer activity as a potential means for male contraception.

developmental biology↗

bioRxiv2023

GenBank genomics highlight the genomic features, genetic diversity and regulation of morphological, metabolic and disease-resistance traits in Nicotiana tabacum

Nicotiana tabacum is a model organism in plant molecular and pathogenic research and has significant potential in the production of biofuels and active pharmaceutical compounds in synthetic biology. Because of the large allotetraploid genome of tobacco, its genomic features, genetic diversity and genetic regulation of many complex traits remain unknown. In this study, we present a nearly complete chromosome-scale assembly of N. tabacum and provide evidence that homoeologous exchange between subgenomes and epigenetic remodelling are likely mechanisms of genome stabilization and subgenome coordination following polyploidization. By leveraging GenBank-scale sequencing and phenotyping data from 5196 lines, geography at the continent scale, rather than types assigned on the basis of curing crop practices, was found to be the most important correlate of genetic structure. Using 178 marker{square}trait associations detected in genome-wide association analysis, a reference genotype-to-phenotype map was built for 39 morphological, developmental, and disease-resistance traits. A novel gene, auxin response factor 9 (Arf9), associated with wider leaves after being knocked out, was fine-mapped to a single nucleotide polymorphism (SNP). This point mutation alters the translated amino acid from Ala203 to Pro203, likely preventing homodimer formation during DNA binding. Our analysis also revealed signatures of positive and polygenic selection for multiple traits during the process of selective breeding. Overall, this study demonstrated the power of leveraging GenBank genomics to gain insights into the genomic features, genetic diversity, and regulation of complex traits in N. tabacum, laying a foundation for future research on plant functional genomics, crop breeding, and the production of biopharmaceuticals and biofuels.

genetics↗

bioRxiv2022

Phenotypical Rescue of Bmp15 Deficiency by Mutation of Inhibin α (inha) Provides Novel Clues to How Bmp15 Controls Zebrafish Folliculogenesis

As an oocyte-specific growth factor, bone morphogenetic protein 15 (BMP15) plays a critical role in controlling folliculogenesis. However, the mechanism of BMP15 action remains elusive. Using zebrafish as the model, we created a bmp15 mutant using CRISPR/Cas9 and demonstrated that bmp15 deficiency caused a significant delay in follicle activation and puberty onset followed by complete arrest of follicle development at previtellogenic stage without yolk accumulation. The mutant females eventually underwent female-to-male sex reversal to become functional males, which was accompanied by a series of changes in secondary sexual characteristics. Interestingly, the blockade of folliculogenesis and sex reversal in bmp15 mutant could be rescued by the loss of inhibin (inha-/-). The follicles of double mutant (bmp15-/-;inha-/-) could progress to mid-vitellogenic stage with yolk accumulation and the fish maintained their femaleness without sex reversal. Transcriptome analysis revealed up-regulation of pathways related to TGF-{beta} signaling and endocytosis in the double mutant follicles. Intriguingly, the expression of inhibin/activin {beta}Aa subunit (inhbaa) increased significantly in the double mutant ovary. Further knockout of inhbaa in the triple mutant (bmp15-/-;inha-/-;inhbaa-/-) resulted in the loss of yolk granules again in the oocytes although the follicles could continue to grow beyond the size range of previtellogenic stage. The serum levels of estradiol (E2) and vitellogenin (Vtg) both decreased significantly in bmp15 single mutant females, returned to normal in the double mutant (bmp15-/-;inha-/-), but reduced again significantly in the triple mutant (bmp15-/-;inha-/-;inhbaa-/-). E2 treatment could rescue the vitellogenic follicles in bmp15-/-, and fadrozole (a nonsteroidal aromatase inhibitor) treatment blocked yolk accumulation in bmp15-/-;inha-/- fish. In summary, the present study provided comprehensive genetic evidence for the interaction of bmp15 pathways and the activin-inhibin system in regulating folliculogenesis, in particular E2 production from the follicle, Vtg biosynthesis in the liver and its update by the developing oocytes.

developmental biology↗

bioRxiv2022

Genetic Analysis of Activin/Inhibin β Subunits in Zebrafish Development and Reproduction

Activin and inhibin are both dimeric proteins sharing the same {beta} subunits that belong to the TGF-{beta} superfamily. They are well known for stimulating and inhibiting pituitary FSH secretion, respectively, in mammals. In addition, activin also acts as a mesoderm-inducing factor in frogs. However, their functions in development and reproduction of other species are poorly defined. In this study, we disrupted all three activin/inhibin {beta} subunits ({beta}Aa, inhbaa; {beta}Ab, inhbab; and {beta}B, inhbb) in zebrafish using CRISPR/Cas9. The loss of {beta}Aa/b but not {beta}B led to a high mortality rate in the post-hatching stage. Surprisingly, the expression of fshb but not lhb in the pituitary increased in the female {beta}A mutant together with aromatase (cyp19a1a) in the ovary. The single mutant of {beta}Aa/b showed normal folliculogenesis in young females; however, their double mutant (inhbaa-/-;inhbab-/-) showed delayed follicle activation, granulosa cell hypertrophy, stromal cell accumulation and tissue fibrosis. The ovary of inhbaa-/- deteriorated progressively after 180 dpf with reduced fecundity and the folliculogenesis ceased completely around 540 dpf. In addition, tumor- or cyst-like tissues started to appear in the inhbaa-/- ovary after about one year. In contrast to females, activin {beta}Aa/b mutant males showed normal spermatogenesis and fertility. As for activin {beta}B subunit, the inhbb-/- mutant exhibited normal folliculogenesis, spermatogenesis and fertility in both sexes; however, the fecundity of mutant females decreased dramatically at 270 dpf with accumulation of early follicles. In summary, the activin-inhibin system plays an indispensable role in fish reproduction, in particular folliculogenesis and ovarian homeostasis.

physiology↗

bioRxiv2022

The trifecta of disease avoidance, silique shattering resistance and flowering period elongation achieved by the BnaIDA editing in Brassica napus

Rapeseed (Brassica napus) oil is a main vegetable oil source in the world. The devastating disease of stem rot caused by the necrotrophic fungus Sclerotinia sclerotiorum and pod shattering led to a great yield loss in Brassica napus. S.sclerotiorum infects the rapeseed by the detached floral petals, in which the released ascospores land and germinate as mycelium, then the petals fall on the leaves at lower part of the rapeseed and heavily attacks the leaves and stems. The prevention of petal-shedding is a promising approach to avoid the stem rot damage, moreover, longer period of flowering time will bring rapeseed flower tourism a huge economic benefit. Notably, IDA (INFLORESCENCE DEFICIENT IN ABSCISSION) and IDA-LIKE(IDL) protein control floral organ abscission in Arabidopsis thaliana. In our study, the precisely editing of two IDA homologues genes using CRISPR/Cas9 system in Brassica napus caused the petal attaching to the flower till pod mature and enhancing the silique dehiscence resistance. Incubating the S.sclerotiorum to petal showed the edited rapeseed avoiding the infection of S.sclerotiorum RNA-Seq analysis demonstrated that in the editted plant, the genes involed in IDA pathway were regulated, while other genes keep unaltered. Investigation of agronomic traits showed that no positive the agronimic traits was introduced in editted plant. Our study demonstrated that mutation of two BnaIDAs creating a promising germplasm for disease avoidance, siliques shattering resistance and flowering period elongation which will contribute great to rapeseed industry.

plant biology↗

bioRxiv2022

Development and Application of a Novel Simple Sequence Repeat Mining Algorithm Based on Regular Expression

Simple sequence repeats (SSRs) are molecular genetic markers that are powerful tools in genomics studies; SSR markers are routinely mined as a part of genetic workflows. Here, we developed a novel SSR mining algorithm based on regular expression that can reduce the complexity of commonly used SSR mining software. We used the following SSR mining regular expression: ({i, j}?) (\1) {k}, where i and j denote the minimum and maximum lengths of the motifs of the SSR sequence, respectively, and k is the minimum number of repeat motifs. From this SSR mining algorithm, we developed an SSR sequence analysis software (named "regexSSRw") that is capable of mining eligible SSR loci from FASTA format sequences; regexSSRw can be accessed at https://github.com/renm79/rgxSSRw. This SSR mining algorithm can aid a range of applications, from being used by programmers in the development of SSR mining software to being implemented by scholars into their SSR marker workflow.

bioinformatics↗

bioRxiv2021

Identification of a novel lineage bat SARS-related coronaviruses that use bat ACE2 receptor

Severe respiratory disease coronavirus-2 (SARS-CoV-2) causes the most devastating disease, COVID-19, of the recent century. One of the unsolved scientific questions around SARS-CoV-2 is the animal origin of this virus. Bats and pangolins are recognized as the most probable reservoir hosts that harbor the highly similar SARS-CoV-2 related viruses (SARSr-CoV-2). Here, we report the identification of a novel lineage of SARSr-CoVs, including RaTG15 and seven other viruses, from bats at the same location where we found RaTG13 in 2015. Although RaTG15 and the related viruses share 97.2% amino acid sequence identities to SARS-CoV-2 in the conserved ORF1b region, but only show less than 77.6% to all known SARSr-CoVs in genome level, thus forms a distinct lineage in the Sarbecovirus phylogenetic tree. We then found that RaTG15 receptor binding domain (RBD) can bind to and use Rhinolophus affinis bat ACE2 (RaACE2) but not human ACE2 as entry receptor, although which contains a short deletion and has different key residues responsible for ACE2 binding. In addition, we show that none of the known viruses in bat SARSr-CoV-2 lineage or the novel lineage discovered so far use human ACE2 efficiently compared to SARSr-CoV-2 from pangolin or some of the SARSr-CoV-1 lineage viruses. Collectively, we suggest more systematic and longitudinal work in bats to prevent future spillover events caused by SARSr-CoVs or to better understand the origin of SARS-CoV-2.

microbiology↗