Biology subjects

Torii, S.

Publications and source records attributed to Torii, S..

At least 19 recordsLinked to original sources

bioRxiv2026

A rapidly deployable CRISPR-Cas3 diagnostic platform for emerging RNA viruses

Rapidly converting viral genome information into deployable molecular tests remains a major challenge in outbreak preparedness. We developed CONAN-SWIFT (Simple Workflow for Isothermal Field Testing), a sequence-to-test platform that integrates computational assay design, reverse-transcription loop-mediated isothermal amplification, CRISPR-Cas3 detection, reagent lyophilization and lateral-flow readout. Sequence-guided assays for Andes virus and Bundibugyo virus were established within approximately three weeks and extended to four additional filoviruses. A web-based designer supported crRNA selection, and systematic RT-LAMP primer optimization improved amplification performance. Recombinant Escherichia coli-expressed Cascade enabled standardized preparation of lyophilized Cas3-detection reagents, which were combined with a battery-operated isothermal device. The portable system detected as few as 10 input RNA copies per reaction within approximately 40 min. It also detected viral RNA and biologically contained, replication-incompetent Ebola virus in spiked human blood and concentrated wastewater. These findings establish the analytical feasibility of a rapidly adaptable CRISPR-Cas3 engineering framework for decentralized detection of emerging RNA viruses.

bioengineering↗

bioRxiv2026

Solvent accessibility of chlorine-reactive amino acid residues in icosahedral virus structures: A meta-analysis

Free chlorine reacts with viral proteins, but the protein structural determinants of viral resistance to chlorine treatment remain poorly understood. Here, we curated a dataset of 498 icosahedral virus structures, including intact virions and virus-like particles (VLPs), from the Protein Data Bank. Surprisingly, only 6.6% of these structures are associated with published viral chlorine inactivation rate constants (kobs). In these matched cases representing 12 virus families, total and maximum solvent accessible surface areas (SASA) of methionine residues within viral attachment and entry proteins correlated significantly with median kobs (Pearsons r = 0.83 and 0.45, respectively; p < 0.05), suggesting a critical role of methionine exposure in viral resistance phenotypes. Across the full curated dataset, fuzzy c-means clustering upon total and maximum SASA profiles of chlorine-reactive residues demonstrates that the common surrogate panel (MS2, PhiX174, Phi6, PRD1, and PR772) fails to represent the SASA diversity of human viruses. Instead, VLPs and novel phages may serve as better surrogates for chlorine treatment due to SASA profile similarities to human viruses. Our findings highlight that residue SASA features provide a quantitative baseline for screening viral resistance to chlorine and offer a data-driven strategy to select structurally representative virus surrogates for future disinfection studies. SYNOPSISSolvent accessibility of chlorine-reactive residues correlates strongly with viral chlorine resistance, providing a robust quantitative metric to compare chlorine resistance phenotypes across viral capsids. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/732355v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@dd6bd1org.highwire.dtl.DTLVardef@d17c53org.highwire.dtl.DTLVardef@1394528org.highwire.dtl.DTLVardef@eb6378_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2026

Systematic Comparison of Indicator and Pathogenic Viruses Using High-Throughput qPCR Identifies Pepper Mild Mottle Virus as a Robust Indicator of Virus Removal in Wastewater Treatment

The selection of appropriate viral indicators for evaluating wastewater treatment performance remains challenging because candidate markers have rarely been compared systematically within a unified analytical framework. Here, we collected influent and effluent samples monthly for one year from two wastewater treatment plants in Japan and conducted, to our knowledge, the first comprehensive comparison of 19 viral targets and one protozoan target using high-throughput quantitative PCR. Pepper mild mottle virus (PMMoV) was consistently detected at high concentrations, showed limited seasonal variability, and exhibited an approximately 1.0 log10 reduction, comparable to those observed for pathogenic viruses. In contrast, Carjivirus, formerly known as crAssphage, was present at the highest concentrations but showed significantly greater reduction than pathogenic viruses. Tomato brown rugose fruit virus (ToBRFV), despite its high abundance and emerging recognition as a potential marker, exhibited pronounced seasonal fluctuations. Other Tobamovirus species, such as cucumber green mottle mosaic virus and tobacco mild green mosaic virus, exhibited similar removal but lower prevalence compared with PMMoV. Overall, PMMoV demonstrated the most balanced performance in terms of abundance, stability, and removal behavior, supporting its use as a robust indicator for monitoring virus removal in wastewater treatment.

microbiology↗

bioRxiv2026

A Capsid Tyrosine Residue Governs the Proteolytic Inactivation of Echovirus 11 in Lakewater

Enteroviruses are environmentally transmissible human pathogens whose stability in natural waters varies widely, yet the molecular determinants underlying this variability remain largely unknown. Echovirus 11 (E11), a re-emerging cause of severe neonatal infections, is efficiently transmitted via contaminated water, making its environmental stability a critical factor in infection risk. Here we identify a single viral capsid residue that governs E11 susceptibility to inactivation by extracellular microbial proteases in freshwater. By combining virus decay measurements in lakewater with proteolytic-cleavage profiling, viral capsid structural analyses, and reverse genetics, we show that the presence of VP2.Y97 renders E11 highly sensitive to microbially-mediated proteolytic decay. Strikingly, this residue is absent from multiple enteroviruses with greater environmental stability, indicating that substitution at a single capsid position is sufficient to shift virus fate in natural waters. These findings reveal that fine-scale capsid architecture controls virus-microbe interactions in aquatic environments and establish a molecular mechanism linking capsid variation to environmental transmission potential among enteroviruses.

microbiology↗

bioRxiv2025

Simultaneous detection of protozoa, bacteria, and viruses from environmental water through membrane-adsorption followed by direct nucleic acid extraction

Waterborne outbreaks caused by protozoan, bacterial, and viral pathogens continue to pose serious public health threats. However, comprehensive monitoring of all three major pathogen types remains uncommon, primarily due to the technical difficulty of simultaneously concentrating and characterizing these diverse microorganisms from a single water sample. Here, we evaluated a membrane adsorption followed by bead-beating-based direct nucleic acid extraction for its sensitivity in detecting waterborne pathogens. We further applied the optimized protocol to river water samples. Our results demonstrated that the use of magnesium chloride in combination with a mixed cellulose ester membrane filter (pore size: 0.8 m) achieved the highest concentration efficiency for Cryptosporidium parvum, Legionella pneumophila, and murine norovirus (MNV), outperforming other methods utilizing the membrane with alternative pore sizes or membrane with another material (i.e., nylon). Furthermore, targeting rRNA of C. parvum instead of rDNA, or incorporating a preamplification step for the L. pneumophila mip gene and MNV, significantly improved the sensitivity. Notably, the 50% limit of detection for C. parvum using our method was comparable to that of traditional immunofluorescent antibody testing. Application of this method to river water further revealed a higher abundance of Bacteroides rRNA markers compared to their corresponding rDNA, underscoring the potential of rRNA-based targets for more sensitive bacterial detection. Importantly, when the target is genomic DNA or RNA, preamplification enables the use of a larger nucleic acids input volume, thereby enhancing sensitivity without introducing measurement bias. Overall, the combination of membrane adsorption and bead-beating-based direct nucleic acid extraction offers a sensitive, all-in-one approach for simultaneous detection of protozoa, bacteria, and viruses in environmental water. This method serves as an effective screening tool for the presence of the three major types of waterborne microorganisms. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=71 SRC="FIGDIR/small/669200v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@d0e9f4org.highwire.dtl.DTLVardef@1afc9fcorg.highwire.dtl.DTLVardef@1f5c355org.highwire.dtl.DTLVardef@1eb14eb_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Lognormal distributions capture site-specific variability in enteric virus concentrations in wastewater

As more data on virus concentrations in influent water from wastewater treatment plants (WWTPs) becomes available, establishing best practices for virus measurements, monitoring, and statistical modelling can improve the understanding of virus concentration distributions in wastewater. To support this, we assessed the temporal variability of norovirus, adenovirus, enterovirus, and rotavirus concentrations in influent water across multiple WWTPs in Switzerland, the USA, and Japan. Our findings demonstrate that the lognormal distribution accurately predicts temporal variations in concentrations for all viruses at all sites, outperforming the gamma and Weibull distributions that do not capture high variability. However, important differences in variability and uncertainty were observed across systems, underscoring the need for site-specific assessments. Using lognormal parameters, we identified optimal monitoring frequencies to balance cost-effectiveness and precision. For most sites, weekly monitoring would be sufficient to estimate the annual average concentration of enteric viruses within a 95% confidence interval of 0.5-log10. We examined the mechanistic basis of the lognormal distribution, highlighting processes that drive its prevalence and shape the behavior of its upper tail. By integrating these insights, this study provides a novel statistical foundation for optimizing virus monitoring frameworks and informing public health interventions targeting wastewater systems.

microbiology↗

bioRxiv2025

Polygenic viral factors enable efficient mosquito-borne transmission of African Zika virus

Zika virus (ZIKV) is a mosquito-borne flavivirus primarily transmitted among humans by Aedes aegypti. Over the past two decades, it has caused significant outbreaks associated with birth defects and neurological disorders. Phylogenetically, ZIKV consists of two main genotypes referred to as the African and Asian lineages, each exhibiting distinct biological properties. African lineage strains are transmitted more efficiently by mosquitoes, but pinpointing the genetic basis of this difference has remained challenging. Here, we address this question by comparing recent African and Asian strains using chimeric viruses, in which segments of the parental genomes are swapped. Our results show that the structural genes from the African strain enhance viral internalization, while the non-structural genes improve genome replication and infectious particle production in mosquito cells. In vivo mosquito transmission is most significantly influenced by the structural genes, although no single viral gene alone determines this effect. Additionally, we develop a stochastic model of in vivo viral dynamics in mosquitoes that mirrors the observed patterns, suggesting that the primary difference between the African and Asian strains lies in their ability to traverse the mosquito salivary glands. Overall, our findings suggest that the polygenic nature of ZIKV transmissibility has prevented Asian lineage strains from achieving the same epidemic potential as African lineage strains, underscoring the importance of lineage-specific adaptive landscapes in shaping ZIKV evolution and emergence.

microbiology↗

bioRxiv2025

Statistical framework for assessing heterogeneous sensitivity of viruses to ultraviolet, ozone, and free chlorine

Disinfection is key to controlling the infection risk caused by viral contaminations. Recent disinfection guidelines often refer to a single virus resistant to the disinfectant of interest, despite a large variation in sensitivity to disinfectants between viruses or even strains within the same species. Here, we show a statistical framework to integrate multiple experimental datasets and measure the variation in sensitivity to disinfectants across different virus species by a parametric distribution, termed the disinfectant sensitivity distribution. To illustrate this framework, we collected 37, 9, and 28 species-dependent inactivation rate constants for ultraviolet (UV), ozone, and free chlorine from systematic reviews, and constructed the sensitivity distributions for those disinfectants. Our approach incorporated the uncertainty in individual inactivation rate constants using a Bayesian framework. The estimated sensitivity distributions suggested that 93.0% (95% CrI: 84.4-97.6%), 99.4% (95% CrI: 86.7-100%), and 90.3% (95% CrI: 78.2-96.6%) of the examined virus species for UV, ozone, and free chlorine are expected to be inactivated by 4-log if the disinfectant dose complies with the values recommended by USEPA Guidelines for 4-log inactivation, respectively. The proposed approach provides a reasonable extrapolation of observed inactivation kinetics to untested viruses and tools for more transparent risk assessments. Graphic for Table of Contents (TOC)/Abstract Art O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=114 SRC="FIGDIR/small/633964v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1215b39org.highwire.dtl.DTLVardef@ec1b90org.highwire.dtl.DTLVardef@1059ee6org.highwire.dtl.DTLVardef@33aac_HPS_FORMAT_FIGEXP M_FIG C_FIG One sentence summaryWe propose a statistical framework to quantify the variation in sensitivity to common disinfectants across virus species synthesizing disinfection data.

microbiology↗

bioRxiv2024

Embryological cellular origins and hypoxia-mediated mechanisms in PIK3CA-Driven refractory vascular malformations

Congenital vascular malformations, affecting 0.5% of the population, often occur in the head and neck, complicating treatment due to the critical functions in these regions. Our previous research identified distinct developmental origins for blood and lymphatic vessels in these areas, tracing them to the cardiopharyngeal mesoderm (CPM), which contributes to the development of the head, neck, and cardiovascular system in both mouse and human embryos. In this study, we investigated the pathogenesis of these malformations by expressing Pik3caH1047R in the CPM. Mice expressing Pik3caH1047R in the CPM developed vascular abnormalities restricted to the head and neck. Single-cell RNA sequencing revealed that Pik3caH1047R upregulates Vegf-a expression in endothelial cells through HIF-mediated hypoxia signaling. Human samples supported these findings, showing elevated HIF-1 and VEGF-A in malformed vessels. Notably, inhibition of HIF-1 and VEGF-A in the mouse model significantly reduced abnormal vasculature. These results highlight the role of embryonic origins and hypoxia-driven mechanisms in vascular malformations, providing a foundation for the development of therapies targeting these difficult-to-treat conditions.

molecular biology↗

bioRxiv2023

Influence of amino acid substitutions in capsid proteins of coxsackievirus B5 on free chlorine and thermal inactivation

The sensitivity of enteroviruses to disinfectants varies among genetically similar variants and coincides with amino acid changes in capsid proteins, though the effect of individual substitutions remains unknown. Here, we employed reverse genetics to investigate how amino acid substitutions in coxsackievirus B5 (CVB5) capsid proteins affect its sensitivity to free chlorine and heat treatment. Of ten amino acid changes hypothesized to coincide with free chlorine resistance, none significantly reduced the chlorine-sensitivity, indicating a minor role of the capsid composition in chlorine sensitivity of CVB5. Conversely, we observed reduced heat sensitivity in mutants with substitutions at the C-terminal region of the viral protein 1. Cryo-electron microscopy revealed that these changes affect the assembly of intermediate viral states (particle A and E), suggesting that the mechanism for reduced heat sensitivity could be related to improved molecular packing of CVB5, resulting in greater stability and/or altered dynamics of virus uncoating during infection.

microbiology↗

bioRxiv2023

Akaluc bioluminescence offers superior sensitivity to track in vivo dynamics of SARS-CoV-2 infection

Monitoring in vivo viral dynamics can improve our understanding of pathogenicity and tissue tropism. For positive-sense, single-stranded RNA viruses, several studies have attempted to monitor viral kinetics in vivo using reporter genomes. The application of such recombinant viruses can be limited by challenges in accommodating bioluminescent reporter genes in the viral genome. Conventional luminescence also exhibits relatively low tissue permeability and thus less sensitivity for visualization in vivo. Here we show that unlike NanoLuc bioluminescence, the improved method, termed AkaBLI, allows visualization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Syrian hamsters. By successfully incorporating a codon-optimized Akaluc luciferase gene into the SARS-CoV-2 genome, we visualized in vivo infection, including the tissue-specific differences associated with particular variants. Additionally, we could evaluate the efficacy of neutralizing antibodies and mRNA vaccination by monitoring changes in Akaluc signals. Overall, AkaBLI is an effective technology for monitoring viral dynamics in live animals.

microbiology↗

bioRxiv2023

The early communication stages between serine proteases and enterovirus capsids in the race for viral disintegration

Enteroviruses are human pathogens known to challenge water safety1,2. Among the microbial stressors found in water, bacterial serine proteases contribute to the control of enterovirus persistence3. However, the structural interactions accounting for the susceptibility of enteroviruses to proteases remains unexplained. Here, we describe the molecular mechanisms involved in the recruitment of serine proteases to viral capsids. Among the virus types used, coxsackievirus A9 (CVA9), but not CVB5 and echovirus 11 (E11), was inactivated by Subtilisin A in a host-independent manner, while Bovine Pancreatic Trypsin (BPT) only reduced CVA9 infectivity in a host-dependent manner. Predictive interaction models of each protease with capsid protomers indicate the main targets as internal disordered protein (IDP) segments exposed either on the 5-fold vertex (DE loop VP1) or at the 5/2-fold intersection (C-terminal end VP1) of viral capsids. We further show that a functional binding protease/capsid depends on both the strength and the evolution over time of protease-VP1 complexes, and lastly on the local adaptation of proteases on surrounding viral regions. Finally, we identified three residues on CVA9 capsid that trigger cleavage by Subtilisin A, one of which acts as a sensor residue contributing to enzyme recognition on the DE loop. Overall, this study describes an important biological mechanism involved in enteroviruses biocontrol.

microbiology↗

bioRxiv2023

ULK1-regulated AMP sensing by AMPK and its application for the treatment of chronic kidney disease

AMP-activated protein kinase (AMPK) is a central kinase involved in energy homeostasis. Increased intracellular adenosine monophosphate (AMP) levels result in AMPK activation through the binding of AMP to the {gamma}-subunit of AMPK. Recently, we reported that AMP-induced AMPK activation is impaired in the kidneys in chronic kidney disease (CKD) despite an increase in the AMP/ATP ratio. However, the mechanisms by which AMP sensing is disrupted in CKD are unclear. In this study, we identified mechanisms of energy homeostasis in which Unc-51-like kinase 1 (ULK1)-dependent phosphorylation of AMPK{gamma}1 at Ser260/Thr262 promotes AMP sensitivity of AMPK. AMPK activation by AMP was impaired in Ulk1-/- mice despite an increased AMP/ATP ratio. We also demonstrated that MK8722, an allosteric AMPK activator, activates AMPK in the kidneys of a CKD mouse model via a pathway that is independent of AMP sensing. MK8722 treatment significantly attenuates the deterioration of renal function in CKD and is a potential therapeutic option in CKD therapeutics.

molecular biology↗

bioRxiv2023

Artificial Intelligence Enables the Label-Free Identification of Chronic Myeloid Leukemia Cells with Mitochondrial Morphological Alterations

Long-term tyrosine kinase inhibitor (TKI) treatment for patients with chronic myeloid leukemia (CML) causes various adverse events. Achieving a deep molecular response (DMR) is necessary for discontinuing TKIs and attaining treatment-free remission. Thus, early diagnosis is crucial as a lower DMR achievement rate has been reported in high-risk patients. Therefore, we attempted to identify CML cells using a novel technology that combines artificial intelligence (AI) with flow cytometry and investigated the basis for AI- mediated identification. Our findings indicate that BCR-ABL1-transduced cells and leukocytes from patients with CML showed significantly fragmented mitochondria and decreased mitochondrial membrane potential. Additionally, BCR-ABL1 enhanced the phosphorylation of Drp1 via the mitogen-activated protein kinase pathway, inducing mitochondrial fragmentation. Finally, the AI identified cell line models and patient leukocytes that showed mitochondrial morphological changes. Our study suggested that this AI- based technology enables the highly sensitive detection of BCR-ABL1-positive cells and early diagnosis of CML.

cancer biology↗

bioRxiv2022

Morphogenesis of bullet-shaped rabies virus particles requires a functional interplay between the viral matrix protein and ESCRT-I component TSG101

Viral protein assembly and virion budding are tightly regulated to enable the proper formation of progeny virions. At this late stage in the virus life cycle, some enveloped viruses take advantage of the host ESCRT (endosomal sorting complex required for transport) machinery, which contributes to the physiological functions of membrane modulation and abscission. Bullet-shaped viral particles are unique morphological characteristics of rhabdoviruses; however, the involvement of host factors in rhabdovirus infection, and specifically the molecular mechanisms underlying virion formation are not fully understood. In the present study, we used a siRNA screening approach and found that the ESCRT-I component TSG101 contributes to the propagation of rabies virus (RABV). We demonstrated that the matrix protein (M) of RABV interacts with TSG101 via the late-domain containing the PY and YL motifs, which are conserved in various viral proteins. Loss of the YL motif in the RABV M or the downregulation of host TSG101 expression resulted in the intracellular aggregation of viral proteins and abnormal virus particle formation, indicating a defect in the RABV assembly and budding processes. These results indicate that the interaction of the RABV M and TSG101 is pivotal for not only the efficient budding of progeny RABV from infected cells but also for the bullet-shaped virion morphology. ImportanceEnveloped-viruses bud from cells with the host lipid bilayer. Generally, the membrane modulation and abscission are mediated by host ESCRT (endosomal sorting complex required for transport) complexes. Some enveloped-viruses utilize their late (L)-domain to interact with ESCRTs, which promotes viral budding. Rhabdoviruses form characteristic bullet-shaped enveloped-virions, but the underlying molecular mechanisms involved remain elusive. Herein, we showed that TSG101, one of ESCRT components, supports rabies virus (RABV) budding and proliferation. TSG101 interacted with RABV matrix protein via L-domain, and the absence of this interaction resulted in intracellular virion accumulation and distortion of the morphology of progeny virions. Our study reveals that virion formation of RABV is highly regulated by TSG101 and the virus matrix protein.

microbiology↗

bioRxiv2022

Molecular diversity and connectivity of accessory olfactory system neurons

Olfaction is the primary sensory modality by which most vertebrate species interpret environmental cues for appropriate behavioral outputs. The olfactory system is subdivided into main (MOS) and accessory (AOS) components which process volatile and non-volatile cues. While much is known regarding the molecular diversity of neurons that comprise the MOS, less is known about the AOS. Here, focusing on the AOS which is largely comprised of the peripheral vomeronasal organ (VNO), the accessory olfactory bulb (AOB) and the medial subnucleus of the amygdala (MeA), we studied the molecular diversity and neuronal subtype connectivity of this interconnected circuit. We show that populations of neurons of the AOS can be molecularly subdivided based on their current or prior expression of the transcription factors Foxp2 or Dbx1. We show that the majority of AOB neurons that project directly to the MeA are of the Foxp2-lineage. Using single cell patch clamp electrophysiology, we further reveal that in addition to sex-specific differences across lineage, the relative contributions of excitatory and inhibitory inputs to MeA Foxp2-lineage neurons differ between sexes. Together, this work uncovers a novel molecular diversity of AOS neurons and lineage- and sex-differences in patterns of connectivity.

neuroscience↗

bioRxiv2022

Observed Kinetics of Enterovirus Inactivation by Free Chlorine Is Host Cell-Dependent

The virucidal efficacy of disinfectants is typically assessed by infectivity assay utilizing a single type of host cell. Enteroviruses infect multiple host cells via different entry routes, and each entry route may be impaired to a varying extent by a given disinfectant. Yet, it is not known how the choice of host cells for titration affects the observed inactivation kinetics. Here, we evaluated the inactivation kinetics of echovirus 11 (E11) by free chlorine, ultraviolet (UV) irradiation, and heat, using three different host cells (BGMK, RD, and A549). E11 inactivation by free chlorine occurred at a two-fold greater rate when enumerated on BGMK cells compared to RD and A549 cells. Conversely, a comparable inactivation rate was observed for UV and heat independent of the host cell used. Host cell-dependent inactivation kinetics by free chlorine were also observed for echovirus 7, 9 and 13, and coxsackievirus A9, confirming that this phenomenon is not serotype-specific. Inactivation of E11 was partly caused by a loss in host cell attachment, which was most pronounced for BGMK cells, and which may be promoted by a lack of CD55 attachment receptors on this cell type. Additionally, BGMK cells lack a key subunit of the uncoating receptor, {beta}2M, which may further contribute to the differential inactivation kinetic for this cell type. Consequently, inactivation kinetics of enteroviruses should be assessed using host cells with different receptor profiles. This will yield a more complete understanding of the inactivating power of disinfectants targeting the viral attachment and/or uncoating. Graphic for Table of Contents (TOC) O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/509468v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@148461eorg.highwire.dtl.DTLVardef@1f3667corg.highwire.dtl.DTLVardef@cd75a3org.highwire.dtl.DTLVardef@e65616_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2022

Characterization of various remdesivir-resistant mutations of SARS-CoV-2 by mathematical modeling and molecular dynamics simulation.

Mutations continue to accumulate within the SARS-CoV-2 genome, and the ongoing epidemic has shown no signs of ending. It is critical to predict problematic mutations that may arise in clinical environments and assess their properties in advance to quickly implement countermeasures against future variant infections. In this study, we identified mutations resistant to remdesivir, which is widely administered to SARS-CoV-2-infected patients, and discuss the cause of resistance. First, we simultaneously constructed eight recombinant viruses carrying the mutations detected in in vitro serial passages of SARS-CoV-2 in the presence of remdesivir. Time course analyses of cellular virus infections showed significantly higher infectious titers and infection rates in mutant viruses than wild type virus under treatment with remdesivir. Next, we developed a mathematical model in consideration of the changing dynamic of cells infected with mutant viruses with distinct propagation properties and defined that mutations detected in in vitro passages canceled the antiviral activities of remdesivir without raising virus production capacity. Finally, molecular dynamics simulations of the NSP12 protein of SARS-CoV-2 revealed that the molecular vibration around the RNA-binding site was increased by the introduction of mutations on NSP12. Taken together, we identified multiple mutations that affected the flexibility of the RNA binding site and decreased the antiviral activity of remdesivir. Our new insights will contribute to developing further antiviral measures against SARS-CoV-2 infection. Significance StatementConsidering the emerging Omicron strain, quick characterization of SARS-CoV-2 mutations is important. However, owing to the difficulties in genetically modifying SARS-CoV-2, limited groups have produced multiple mutant viruses. Our cutting-edge reverse genetics technique enabled construction of eight reporter-carrying mutant SARS-CoV-2 in this study. We developed a mathematical model taking into account sequential changes and identified antiviral effects against mutant viruses with differing propagation capacities and lethal effects on cells. In addition to identifying the positions of mutations, we analyzed the structural changes in SARS-CoV-2 NSP12 by computer simulation to understand the mechanism of resistance. This multidisciplinary approach promotes the evaluation of future resistance mutations.

microbiology↗