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Desai SK, Zhou Y, Dilawari R, Routh AL, Popov V, Kenney LJ. RpoS activates formation of Salmonella Typhi biofilms and drives persistence in the gall bladder. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.26.564249. [PMID: 37961640 PMCID: PMC10634867 DOI: 10.1101/2023.10.26.564249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The development of strategies for targeting the asymptomatic carriage of Salmonella Typhi in chronic typhoid patients has suffered owing to our basic lack of understanding of the molecular mechanisms that enable the formation of S. Typhi biofilms. Traditionally, studies have relied on cholesterol-attached biofilms formed by a closely related serovar, Typhimurium, to mimic multicellular Typhi communities formed on human gallstones. In long-term infections, S. Typhi adopts the biofilm lifestyle to persist in vivo and survive in the carrier state, ultimately leading to the spread of infections via the fecal-oral route of transmission. In the present work, we studied S. Typhi biofilms directly, applied targeted as well as genome-wide genetic approaches to uncover unique biofilm components that do not conform to the CsgD-dependent pathway established in S. Typhimurium. We undertook a genome-wide Tn5 mutation screen in a highly successful parental lineage of S. Typhi, strain H58, in gallstone-mimicking conditions. We generated New Generation Sequencing libraries based on the ClickSeq technology to identify the key regulators, IraP and RpoS, and the matrix components as Sth fimbriae, Vi capsule and lipopolysaccharide. We discovered that the starvation sigma factor, RpoS, was required for the transcriptional activation of matrix-encoding genes in vitro, and for S. Typhi colonization in persistent infections in vivo, using a heterologous fish larval model. An rpoS null mutant failed to colonize the gall bladder in chronic zebrafish infections. Overall, our work uncovered a novel RpoS-driven paradigm for the formation of cholesterol-attached Typhi biofilms, and emphasized the role(s) of stress signaling pathways for adaptation in chronic infections. Our identification of the biofilm regulators in S. Typhi paves the way for the development of drugs against typhoid carriage, which will ultimately control the increased incidence of gall bladder cancer in typhoid carriers.
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Oyola S. Characterization of SARS-CoV-2 genetic evolution in vaccinated and non-vaccinated patients from the Kenyan population. RESEARCH SQUARE 2023:rs.3.rs-3457875. [PMID: 37961584 PMCID: PMC10635312 DOI: 10.21203/rs.3.rs-3457875/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Vaccination is a key control measure of COVID-19 by preventing severe effects of disease outcomes, reducing hospitalization rates and death, and increasing herd immunity. However, vaccination can affect the evolution and adaptation of SARS-CoV-2, largely through vaccine-induced immune pressure. Here we investigated the recombination events and single nucleotide polymorphisms (SNPs) on SARS-CoV-2 genome in non-vaccinated and vaccinated patients in the Kenyan population. We identified recombination hotspots in the S, N, and ORF1a/b genes and showed the genetic evolution landscape of SARS-CoV-2 by comparing within-wave and inter-wave recombination events from the beginning of the pandemic (June 2020) to (October 2022) in Kenya. An in-depth analysis of (SNPs) on the S, ORf1a/b, and N genes identified previously unreported mutations. We detected a minority variant in non-vaccinated patients in Kenya, that contained immune escape mutation S255F of the spike gene and showing a differential recombination pattern within the non-vaccinated patients. Detailed analysis of recombination between waves suggested an association between increased population immunity and declining risk of emergence of variants of concern. Overall, this work identified unique mutations in SARS-CoV-2 which could have significant implications for virus evolution, virulence, and immune escape.
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Zheng P, Zhou C, Ding Y, Liu B, Lu L, Zhu F, Duan S. Nanopore sequencing technology and its applications. MedComm (Beijing) 2023; 4:e316. [PMID: 37441463 PMCID: PMC10333861 DOI: 10.1002/mco2.316] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 07/15/2023] Open
Abstract
Since the development of Sanger sequencing in 1977, sequencing technology has played a pivotal role in molecular biology research by enabling the interpretation of biological genetic codes. Today, nanopore sequencing is one of the leading third-generation sequencing technologies. With its long reads, portability, and low cost, nanopore sequencing is widely used in various scientific fields including epidemic prevention and control, disease diagnosis, and animal and plant breeding. Despite initial concerns about high error rates, continuous innovation in sequencing platforms and algorithm analysis technology has effectively addressed its accuracy. During the coronavirus disease (COVID-19) pandemic, nanopore sequencing played a critical role in detecting the severe acute respiratory syndrome coronavirus-2 virus genome and containing the pandemic. However, a lack of understanding of this technology may limit its popularization and application. Nanopore sequencing is poised to become the mainstream choice for preventing and controlling COVID-19 and future epidemics while creating value in other fields such as oncology and botany. This work introduces the contributions of nanopore sequencing during the COVID-19 pandemic to promote public understanding and its use in emerging outbreaks worldwide. We discuss its application in microbial detection, cancer genomes, and plant genomes and summarize strategies to improve its accuracy.
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Affiliation(s)
- Peijie Zheng
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Chuntao Zhou
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Yuemin Ding
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
| | - Bin Liu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Liuyi Lu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Feng Zhu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Shiwei Duan
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
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Zhou T, Gilliam NJ, Li S, Spandau S, Osborn RM, Connor S, Anderson CS, Mariani TJ, Thakar J, Dewhurst S, Mathews DH, Huang L, Sun Y. Generation and Functional Analysis of Defective Viral Genomes during SARS-CoV-2 Infection. mBio 2023; 14:e0025023. [PMID: 37074178 PMCID: PMC10294654 DOI: 10.1128/mbio.00250-23] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/28/2023] [Indexed: 04/20/2023] Open
Abstract
Defective viral genomes (DVGs) have been identified in many RNA viruses as a major factor influencing antiviral immune response and viral pathogenesis. However, the generation and function of DVGs in SARS-CoV-2 infection are less known. In this study, we elucidated DVG generation in SARS-CoV-2 and its relationship with host antiviral immune response. We observed DVGs ubiquitously from transcriptome sequencing (RNA-seq) data sets of in vitro infections and autopsy lung tissues of COVID-19 patients. Four genomic hot spots were identified for DVG recombination, and RNA secondary structures were suggested to mediate DVG formation. Functionally, bulk and single-cell RNA-seq analysis indicated the interferon (IFN) stimulation of SARS-CoV-2 DVGs. We further applied our criteria to the next-generation sequencing (NGS) data set from a published cohort study and observed a significantly higher amount and frequency of DVG in symptomatic patients than those in asymptomatic patients. Finally, we observed exceptionally diverse DVG populations in one immunosuppressive patient up to 140 days after the first positive test of COVID-19, suggesting for the first time an association between DVGs and persistent viral infections in SARS-CoV-2. Together, our findings strongly suggest a critical role of DVGs in modulating host IFN responses and symptom development, calling for further inquiry into the mechanisms of DVG generation and into how DVGs modulate host responses and infection outcome during SARS-CoV-2 infection. IMPORTANCE Defective viral genomes (DVGs) are generated ubiquitously in many RNA viruses, including SARS-CoV-2. Their interference activity to full-length viruses and IFN stimulation provide the potential for them to be used in novel antiviral therapies and vaccine development. SARS-CoV-2 DVGs are generated through the recombination of two discontinuous genomic fragments by viral polymerase complex, and this recombination is also one of the major mechanisms for the emergence of new coronaviruses. Focusing on the generation and function of SARS-CoV-2 DVGs, these studies identify new hot spots for nonhomologous recombination and strongly suggest that the secondary structures within viral genomes mediate the recombination. Furthermore, these studies provide the first evidence for IFN stimulation activity of de novo DVGs during natural SARS-CoV-2 infection. These findings set up the foundation for further mechanism studies of SARS-CoV-2 recombination and provide evidence to harness the immunostimulatory potential of DVGs in the development of a vaccine and antivirals for SARS-CoV-2.
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Affiliation(s)
- Terry Zhou
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
| | - Nora J. Gilliam
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
- Medical Scientist Training Program, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- Translational Biomedical Sciences PhD Program, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Sizhen Li
- School of Electrical Engineering & Computer Science, Oregon State University, Corvallis, Oregon, USA
| | - Simone Spandau
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
| | - Raven M. Osborn
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
- Translational Biomedical Sciences PhD Program, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Sarah Connor
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester, Rochester, New York, USA
| | - Christopher S. Anderson
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester, Rochester, New York, USA
| | - Thomas J. Mariani
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester, Rochester, New York, USA
| | - Juilee Thakar
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Stephen Dewhurst
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
| | - David H. Mathews
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York, USA
| | - Liang Huang
- School of Electrical Engineering & Computer Science, Oregon State University, Corvallis, Oregon, USA
| | - Yan Sun
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
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Sotcheff S, Zhou Y, Yeung J, Sun Y, Johnson JE, Torbett BE, Routh AL. ViReMa: a virus recombination mapper of next-generation sequencing data characterizes diverse recombinant viral nucleic acids. Gigascience 2023; 12:giad009. [PMID: 36939008 PMCID: PMC10025937 DOI: 10.1093/gigascience/giad009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 11/30/2022] [Accepted: 02/03/2023] [Indexed: 03/21/2023] Open
Abstract
BACKGROUND Genetic recombination is a tremendous source of intrahost diversity in viruses and is critical for their ability to rapidly adapt to new environments or fitness challenges. While viruses are routinely characterized using high-throughput sequencing techniques, characterizing the genetic products of recombination in next-generation sequencing data remains a challenge. Viral recombination events can be highly diverse and variable in nature, including simple duplications and deletions, or more complex events such as copy/snap-back recombination, intervirus or intersegment recombination, and insertions of host nucleic acids. Due to the variable mechanisms driving virus recombination and the different selection pressures acting on the progeny, recombination junctions rarely adhere to simple canonical sites or sequences. Furthermore, numerous different events may be present simultaneously in a viral population, yielding a complex mutational landscape. FINDINGS We have previously developed an algorithm called ViReMa (Virus Recombination Mapper) that bootstraps the bowtie short-read aligner to capture and annotate a wide range of recombinant species found within virus populations. Here, we have updated ViReMa to provide an "error density" function designed to accurately detect recombination events in the longer reads now routinely generated by the Illumina platforms and provide output reports for multiple types of recombinant species using standardized formats. We demonstrate the utility and flexibility of ViReMa in different settings to report deletion events in simulated data from Flock House virus, copy-back RNA species in Sendai viruses, short duplication events in HIV, and virus-to-host recombination in an archaeal DNA virus.
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Affiliation(s)
- Stephanea Sotcheff
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Yiyang Zhou
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jason Yeung
- John Sealy School of Medicine, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Yan Sun
- Department of Microbiology and Immunology, The University of Rochester Medical Center, Rochester, NY 14642, USA
| | - John E Johnson
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
| | - Bruce E Torbett
- Department of Pediatrics, School of Medicine, University of Washington, Seattle, WA 98105, USA
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA 98105, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195, USA
| | - Andrew L Routh
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
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Zhou T, Gilliam NJ, Li S, Spaudau S, Osborn RM, Anderson CS, Mariani TJ, Thakar J, Dewhurst S, Mathews DH, Huang L, Sun Y. Generation and functional analysis of defective viral genomes during SARS-CoV-2 infection.. [PMID: 36172120 PMCID: PMC9516852 DOI: 10.1101/2022.09.22.509123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Defective viral genomes (DVGs) have been identified in many RNA viruses as a major factor influencing antiviral immune response and viral pathogenesis. However, the generation and function of DVGs in SARS-CoV-2 infection are less known. In this study, we elucidated DVG generation in SARS-CoV-2 and its relationship with host antiviral immune response. We observed DVGs ubiquitously from RNA-seq datasets of in vitro infections and autopsy lung tissues of COVID-19 patients. Four genomic hotspots were identified for DVG recombination and RNA secondary structures were suggested to mediate DVG formation. Functionally, bulk and single cell RNA-seq analysis indicated the IFN stimulation of SARS-CoV-2 DVGs. We further applied our criteria to the NGS dataset from a published cohort study and observed significantly higher DVG amount and frequency in symptomatic patients than that in asymptomatic patients. Finally, we observed unusually high DVG frequency in one immunosuppressive patient up to 140 days after admitted to hospital due to COVID-19, first-time suggesting an association between DVGs and persistent viral infections in SARS-CoV-2. Together, our findings strongly suggest a critical role of DVGs in modulating host IFN responses and symptom development, calling for further inquiry into the mechanisms of DVG generation and how DVGs modulate host responses and infection outcome during SARS-CoV-2 infection.
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7
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Vu MN, Lokugamage KG, Plante JA, Scharton D, Bailey AO, Sotcheff S, Swetnam DM, Johnson BA, Schindewolf C, Alvarado RE, Crocquet-Valdes PA, Debbink K, Weaver SC, Walker DH, Russell WK, Routh AL, Plante KS, Menachery VD. QTQTN motif upstream of the furin-cleavage site plays a key role in SARS-CoV-2 infection and pathogenesis. Proc Natl Acad Sci U S A 2022; 119:e2205690119. [PMID: 35881779 PMCID: PMC9371735 DOI: 10.1073/pnas.2205690119] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/26/2022] [Indexed: 02/08/2023] Open
Abstract
The furin cleavage site (FCS), an unusual feature in the SARS-CoV-2 spike protein, has been spotlighted as a factor key to facilitating infection and pathogenesis by increasing spike processing. Similarly, the QTQTN motif directly upstream of the FCS is also an unusual feature for group 2B coronaviruses (CoVs). The QTQTN deletion has consistently been observed in in vitro cultured virus stocks and some clinical isolates. To determine whether the QTQTN motif is critical to SARS-CoV-2 replication and pathogenesis, we generated a mutant deleting the QTQTN motif (ΔQTQTN). Here, we report that the QTQTN deletion attenuates viral replication in respiratory cells in vitro and attenuates disease in vivo. The deletion results in a shortened, more rigid peptide loop that contains the FCS and is less accessible to host proteases, such as TMPRSS2. Thus, the deletion reduced the efficiency of spike processing and attenuates SARS-CoV-2 infection. Importantly, the QTQTN motif also contains residues that are glycosylated, and disruption of its glycosylation also attenuates virus replication in a TMPRSS2-dependent manner. Together, our results reveal that three aspects of the S1/S2 cleavage site-the FCS, loop length, and glycosylation-are required for efficient SARS-CoV-2 replication and pathogenesis.
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Affiliation(s)
- Michelle N. Vu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555
| | - Kumari G. Lokugamage
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555
| | - Jessica A. Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX 77555
| | - Dionna Scharton
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX 77555
| | - Aaron O. Bailey
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555
| | - Stephanea Sotcheff
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555
| | - Daniele M. Swetnam
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555
| | - Bryan A. Johnson
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555
| | - Craig Schindewolf
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555
| | - R. Elias Alvarado
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX
| | | | - Kari Debbink
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21211
| | - Scott C. Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX 77555
- Center for Biodefense and Emerging Infectious Disease, University of Texas Medical Branch, Galveston, TX 77555
| | - David H. Walker
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555
- Center for Biodefense and Emerging Infectious Disease, University of Texas Medical Branch, Galveston, TX 77555
| | - William K. Russell
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555
| | - Andrew L. Routh
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555
| | - Kenneth S. Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX 77555
| | - Vineet D. Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX 77555
- Center for Biodefense and Emerging Infectious Disease, University of Texas Medical Branch, Galveston, TX 77555
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Yeung J, Routh AL. ViReMaShiny: an interactive application for analysis of viral recombination data. Bioinformatics 2022; 38:4420-4422. [PMID: 35904541 PMCID: PMC9477530 DOI: 10.1093/bioinformatics/btac522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/15/2022] [Accepted: 07/21/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Recombination is an essential driver of virus evolution and adaption, giving rise to new chimeric viruses, structural variants, sub-genomic RNAs and defective RNAs. Next-generation sequencing (NGS) of virus samples, either from experimental or clinical settings, has revealed a complex distribution of recombination events that contributes to intrahost diversity. We and others have previously developed alignment tools to discover and map these diverse recombination events in NGS data. However, there is no standard for data visualization to contextualize events of interest, and downstream analysis often requires bespoke coding. RESULTS We present ViReMaShiny, a web-based application built using the R Shiny framework to allow interactive exploration and point-and-click visualization of viral recombination data provided in BED format generated by computational pipelines such as ViReMa (Viral-Recombination-Mapper). AVAILABILITY AND IMPLEMENTATION The application is hosted at https://routhlab.shinyapps.io/ViReMaShiny/ with associated documentation at https://jayeung12.github.io/. Code is available at https://github.com/routhlab/ViReMaShiny. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jason Yeung
- John Sealy School of Medicine, The University of Texas Medical Branch, Galveston, TX 77550, USA
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9
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Johnson BA, Zhou Y, Lokugamage KG, Vu MN, Bopp N, Crocquet-Valdes PA, Kalveram B, Schindewolf C, Liu Y, Scharton D, Plante JA, Xie X, Aguilar P, Weaver SC, Shi PY, Walker DH, Routh AL, Plante KS, Menachery VD. Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis. PLoS Pathog 2022; 18:e1010627. [PMID: 35728038 PMCID: PMC9275689 DOI: 10.1371/journal.ppat.1010627] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/12/2022] [Accepted: 05/30/2022] [Indexed: 12/27/2022] Open
Abstract
While SARS-CoV-2 continues to adapt for human infection and transmission, genetic variation outside of the spike gene remains largely unexplored. This study investigates a highly variable region at residues 203-205 in the SARS-CoV-2 nucleocapsid protein. Recreating a mutation found in the alpha and omicron variants in an early pandemic (WA-1) background, we find that the R203K+G204R mutation is sufficient to enhance replication, fitness, and pathogenesis of SARS-CoV-2. The R203K+G204R mutant corresponds with increased viral RNA and protein both in vitro and in vivo. Importantly, the R203K+G204R mutation increases nucleocapsid phosphorylation and confers resistance to inhibition of the GSK-3 kinase, providing a molecular basis for increased virus replication. Notably, analogous alanine substitutions at positions 203+204 also increase SARS-CoV-2 replication and augment phosphorylation, suggesting that infection is enhanced through ablation of the ancestral 'RG' motif. Overall, these results demonstrate that variant mutations outside spike are key components in SARS-CoV-2's continued adaptation to human infection.
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Affiliation(s)
- Bryan A Johnson
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Yiyang Zhou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kumari G Lokugamage
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Michelle N Vu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Nathen Bopp
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | | | - Birte Kalveram
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Craig Schindewolf
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Yang Liu
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Dionna Scharton
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Jessica A Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Patricia Aguilar
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Scott C Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Drug Discovery, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - David H Walker
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Andrew L Routh
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kenneth S Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Vineet D Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
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10
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Olmo-Uceda MJ, Muñoz-Sánchez JC, Lasso-Giraldo W, Arnau V, Díaz-Villanueva W, Elena SF. DVGfinder: A Metasearch Tool for Identifying Defective Viral Genomes in RNA-Seq Data. Viruses 2022; 14:v14051114. [PMID: 35632855 PMCID: PMC9144107 DOI: 10.3390/v14051114] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/18/2022] [Accepted: 05/20/2022] [Indexed: 02/05/2023] Open
Abstract
The generation of different types of defective viral genomes (DVG) is an unavoidable consequence of the error-prone replication of RNA viruses. In recent years, a particular class of DVGs, those containing long deletions or genome rearrangements, has gain interest due to their potential therapeutic and biotechnological applications. Identifying such DVGs in high-throughput sequencing (HTS) data has become an interesting computational problem. Several algorithms have been proposed to accomplish this goal, though all incur false positives, a problem of practical interest if such DVGs have to be synthetized and tested in the laboratory. We present a metasearch tool, DVGfinder, that wraps the two most commonly used DVG search algorithms in a single workflow for the identification of the DVGs in HTS data. DVGfinder processes the results of ViReMa-a and DI-tector and uses a gradient boosting classifier machine learning algorithm to reduce the number of false-positive events. The program also generates output files in user-friendly HTML format, which can help users to explore the DVGs identified in the sample. We evaluated the performance of DVGfinder compared to the two search algorithms used separately and found that it slightly improves sensitivities for low-coverage synthetic HTS data and DI-tector precision for high-coverage samples. The metasearch program also showed higher sensitivity on a real sample for which a set of copy-backs were previously validated.
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Affiliation(s)
- Maria J. Olmo-Uceda
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, 46980 Valencia, Spain; (M.J.O.-U.); (J.C.M.-S.); (W.L.-G.); (V.A.); (W.D.-V.)
| | - Juan C. Muñoz-Sánchez
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, 46980 Valencia, Spain; (M.J.O.-U.); (J.C.M.-S.); (W.L.-G.); (V.A.); (W.D.-V.)
| | - Wilberth Lasso-Giraldo
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, 46980 Valencia, Spain; (M.J.O.-U.); (J.C.M.-S.); (W.L.-G.); (V.A.); (W.D.-V.)
| | - Vicente Arnau
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, 46980 Valencia, Spain; (M.J.O.-U.); (J.C.M.-S.); (W.L.-G.); (V.A.); (W.D.-V.)
| | - Wladimiro Díaz-Villanueva
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, 46980 Valencia, Spain; (M.J.O.-U.); (J.C.M.-S.); (W.L.-G.); (V.A.); (W.D.-V.)
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, 46980 Valencia, Spain; (M.J.O.-U.); (J.C.M.-S.); (W.L.-G.); (V.A.); (W.D.-V.)
- Santa Fe Institute, Santa Fe, NM 87501, USA
- Correspondence: ; Tel.: +34-963-544-779
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11
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Wang H, Cui X, Cai X, An T. Recombination in Positive-Strand RNA Viruses. Front Microbiol 2022; 13:870759. [PMID: 35663855 PMCID: PMC9158499 DOI: 10.3389/fmicb.2022.870759] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/21/2022] [Indexed: 12/28/2022] Open
Abstract
RNA recombination is a major driver of genetic shifts tightly linked to the evolution of RNA viruses. Genomic recombination contributes substantially to the emergence of new viral lineages, expansion in host tropism, adaptations to new environments, and virulence and pathogenesis. Here, we review some of the recent progress that has advanced our understanding of recombination in positive-strand RNA viruses, including recombination triggers and the mechanisms behind them. The study of RNA recombination aids in predicting the probability and outcome of viral recombination events, and in the design of viruses with reduced recombination frequency as candidates for the development of live attenuated vaccines. Surveillance of viral recombination should remain a priority in the detection of emergent viral strains, a goal that can only be accomplished by expanding our understanding of how these events are triggered and regulated.
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Affiliation(s)
| | | | | | - Tongqing An
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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12
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Zhou Y, Sotcheff SL, Routh AL. Next-generation sequencing: A new avenue to understand viral RNA-protein interactions. J Biol Chem 2022; 298:101924. [PMID: 35413291 PMCID: PMC8994257 DOI: 10.1016/j.jbc.2022.101924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 04/01/2022] [Accepted: 04/02/2022] [Indexed: 10/25/2022] Open
Abstract
The genomes of RNA viruses present an astonishing source of both sequence and structural diversity. From intracellular viral RNA-host interfaces to interactions between the RNA genome and structural proteins in virus particles themselves, almost the entire viral lifecycle is accompanied by a myriad of RNA-protein interactions that are required to fulfill their replicative potential. It is therefore important to characterize such rich and dynamic collections of viral RNA-protein interactions to understand virus evolution and their adaptation to their hosts and environment. Recent advances in next-generation sequencing technologies have allowed the characterization of viral RNA-protein interactions, including both transient and conserved interactions, where molecular and structural approaches have fallen short. In this review, we will provide a methodological overview of the high-throughput techniques used to study viral RNA-protein interactions, their biochemical mechanisms, and how they evolved from classical methods as well as one another. We will discuss how different techniques have fueled virus research to characterize how viral RNA and proteins interact, both locally and on a global scale. Finally, we will present examples on how these techniques influence the studies of clinically important pathogens such as HIV-1 and SARS-CoV-2.
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Affiliation(s)
- Yiyang Zhou
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA.
| | - Stephanea L Sotcheff
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Andrew L Routh
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA; Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, Texas, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
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13
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Nielsen MC, Machado RRG, Mitchell BM, McConnell AJ, Saada NI, Weaver SC, Ren P. A Comparison of Seegene Technologies Novaplex SARS-CoV-2 Variants I, II, and IV Assays with Spike Gene Sequencing for Detection of Known Severe Acute Respiratory Syndrome Coronavirus 2 Variants. J Mol Diagn 2022; 24:455-461. [PMID: 35218945 PMCID: PMC8865930 DOI: 10.1016/j.jmoldx.2022.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 02/02/2022] [Accepted: 02/11/2022] [Indexed: 01/13/2023] Open
Abstract
Tracking new and emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has become increasingly important for public health responses, primarily because of variant-dependent transmission, disease severity, and treatment decisions. This evaluation compared Seegene Technologies Novaplex SARS-CoV-2 Variants I, II, and IV (I,II&IV) assays to detect known SARS-CoV-2 variants using traditional spike gene Sanger sequencing results as the gold standard reference. Both RNA extraction and extraction-free protocols were assessed. A total of 156 samples were included in this study. There was 100% (109/109) overall agreement (95% CI, 96.7%-100%) between the spike gene sequencing and the I,II&IV results using extracted RNA for the variants included in the Novaplex assay menus. The RNA extraction-free method was 91.7% (143/156) as sensitive (95% CI, 86.2%-95.5%) as the traditional RNA extraction method. Using the extraction-free method on samples with higher cycle threshold values (>30) resulted in some mutations not being detected, presumably due to lower nucleic acid concentrations in the original samples. In conclusion, the I,II&IV assays provide an accurate, rapid, and less labor-intensive method for detecting SARS-CoV-2 and identifying known variants of interest and concern. The RNA extraction-free method for samples with cycle threshold of <30 could be cost-effective for surveillance purposes. However, spike gene sequencing retains the advantage of detecting more and new variants.
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Affiliation(s)
- Marisa C Nielsen
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas
| | - Rafael R G Machado
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas; Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Brooke M Mitchell
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas
| | - Allan J McConnell
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas
| | - Nehad I Saada
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas
| | - Scott C Weaver
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas
| | - Ping Ren
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas.
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14
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Muruato A, Vu MN, Johnson BA, Davis-Gardner ME, Vanderheiden A, Lokugamage K, Schindewolf C, Crocquet-Valdes PA, Langsjoen RM, Plante JA, Plante KS, Weaver SC, Debbink K, Routh AL, Walker D, Suthar MS, Shi PY, Xie X, Menachery VD. Mouse-adapted SARS-CoV-2 protects animals from lethal SARS-CoV challenge. PLoS Biol 2021; 19:e3001284. [PMID: 34735434 PMCID: PMC8594810 DOI: 10.1371/journal.pbio.3001284] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 11/16/2021] [Accepted: 10/17/2021] [Indexed: 01/16/2023] Open
Abstract
The emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has resulted in a pandemic causing significant damage to public health and the economy. Efforts to understand the mechanisms of Coronavirus Disease 2019 (COVID-19) have been hampered by the lack of robust mouse models. To overcome this barrier, we used a reverse genetic system to generate a mouse-adapted strain of SARS-CoV-2. Incorporating key mutations found in SARS-CoV-2 variants, this model recapitulates critical elements of human infection including viral replication in the lung, immune cell infiltration, and significant in vivo disease. Importantly, mouse adaptation of SARS-CoV-2 does not impair replication in human airway cells and maintains antigenicity similar to human SARS-CoV-2 strains. Coupled with the incorporation of mutations found in variants of concern, CMA3p20 offers several advantages over other mouse-adapted SARS-CoV-2 strains. Using this model, we demonstrate that SARS-CoV-2-infected mice are protected from lethal challenge with the original Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), suggesting immunity from heterologous Coronavirus (CoV) strains. Together, the results highlight the use of this mouse model for further study of SARS-CoV-2 infection and disease.
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Affiliation(s)
- Antonio Muruato
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Michelle N. Vu
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Bryan A. Johnson
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Meredith E. Davis-Gardner
- Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Abigail Vanderheiden
- Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Kumari Lokugamage
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Craig Schindewolf
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | | | - Rose M. Langsjoen
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Jessica A. Plante
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kenneth S. Plante
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Scott C. Weaver
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kari Debbink
- Department of Natural Science, Bowie State University, Bowie, Maryland, United States of America
| | - Andrew L. Routh
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - David Walker
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Mehul S. Suthar
- Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Yerkes National Primate Research Center, Atlanta, Georgia, United States of America
| | - Pei-Yong Shi
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Xuping Xie
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Vineet D. Menachery
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
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15
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Johnson BA, Zhou Y, Lokugamage KG, Vu MN, Bopp N, Crocquet-Valdes PA, Schindewolf C, Liu Y, Scharton D, Plante JA, Xie X, Aguilar P, Weaver SC, Shi PY, Walker DH, Routh AL, Plante KS, Menachery VD. Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34671771 PMCID: PMC8528077 DOI: 10.1101/2021.10.14.464390] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
While SARS-CoV-2 continues to adapt for human infection and transmission, genetic variation outside of the spike gene remains largely unexplored. This study investigates a highly variable region at residues 203–205 in the SARS-CoV-2 nucleocapsid protein. Recreating a mutation found in the alpha and omicron variants in an early pandemic (WA-1) background, we find that the R203K+G204R mutation is sufficient to enhance replication, fitness, and pathogenesis of SARS-CoV-2. The R203K+G204R mutant corresponds with increased viral RNA and protein both in vitro and in vivo. Importantly, the R203K+G204R mutation increases nucleocapsid phosphorylation and confers resistance to inhibition of the GSK-3 kinase, providing a molecular basis for increased virus replication. Notably, analogous alanine substitutions at positions 203+204 also increase SARS-CoV-2 replication and augment phosphorylation, suggesting that infection is enhanced through ablation of the ancestral ‘RG’ motif. Overall, these results demonstrate that variant mutations outside spike are key components in SARS-CoV-2’s continued adaptation to human infection.
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16
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Long S. SARS-CoV-2 Subgenomic RNAs: Characterization, Utility, and Perspectives. Viruses 2021; 13:v13101923. [PMID: 34696353 PMCID: PMC8539008 DOI: 10.3390/v13101923] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/12/2021] [Accepted: 09/16/2021] [Indexed: 12/11/2022] Open
Abstract
SARS-CoV-2, the etiologic agent at the root of the ongoing COVID-19 pandemic, harbors a large RNA genome from which a tiered ensemble of subgenomic RNAs (sgRNAs) is generated. Comprehensive definition and investigation of these RNA products are important for understanding SARS-CoV-2 pathogenesis. This review summarizes the recent progress on SARS-CoV-2 sgRNA identification, characterization, and application as a viral replication marker. The significance of these findings and potential future research areas of interest are discussed.
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Affiliation(s)
- Samuel Long
- Independent Researcher, Clarksburg, MD 20871, USA
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