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Iketani S, Ho DD. SARS-CoV-2 resistance to monoclonal antibodies and small-molecule drugs. Cell Chem Biol 2024; 31:632-657. [PMID: 38640902 PMCID: PMC11084874 DOI: 10.1016/j.chembiol.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/21/2024]
Abstract
Over four years have passed since the beginning of the COVID-19 pandemic. The scientific response has been rapid and effective, with many therapeutic monoclonal antibodies and small molecules developed for clinical use. However, given the ability for viruses to become resistant to antivirals, it is perhaps no surprise that the field has identified resistance to nearly all of these compounds. Here, we provide a comprehensive review of the resistance profile for each of these therapeutics. We hope that this resource provides an atlas for mutations to be aware of for each agent, particularly as a springboard for considerations for the next generation of antivirals. Finally, we discuss the outlook and thoughts for moving forward in how we continue to manage this, and the next, pandemic.
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Affiliation(s)
- Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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Farooq T, Hussain MD, Shakeel MT, Riaz H, Waheed U, Siddique M, Shahzadi I, Aslam MN, Tang Y, She X, He Z. Global genetic diversity and evolutionary patterns among Potato leafroll virus populations. Front Microbiol 2022; 13:1022016. [PMID: 36590416 PMCID: PMC9801716 DOI: 10.3389/fmicb.2022.1022016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/12/2022] [Indexed: 01/04/2023] Open
Abstract
Potato leafroll virus (PLRV) is a widespread and one of the most damaging viral pathogens causing significant quantitative and qualitative losses in potato worldwide. The current knowledge of the geographical distribution, standing genetic diversity and the evolutionary patterns existing among global PLRV populations is limited. Here, we employed several bioinformatics tools and comprehensively analyzed the diversity, genomic variability, and the dynamics of key evolutionary factors governing the global spread of this viral pathogen. To date, a total of 84 full-genomic sequences of PLRV isolates have been reported from 22 countries with most genomes documented from Kenya. Among all PLRV-encoded major proteins, RTD and P0 displayed the highest level of nucleotide variability. The highest percentage of mutations were associated with RTD (38.81%) and P1 (31.66%) in the coding sequences. We detected a total of 10 significantly supported recombination events while the most frequently detected ones were associated with PLRV genome sequences reported from Kenya. Notably, the distribution patterns of recombination breakpoints across different genomic regions of PLRV isolates remained variable. Further analysis revealed that with exception of a few positively selected codons, a major part of the PLRV genome is evolving under strong purifying selection. Protein disorder prediction analysis revealed that CP-RTD had the highest percentage (48%) of disordered amino acids and the majority (27%) of disordered residues were positioned at the C-terminus. These findings will extend our current knowledge of the PLRV geographical prevalence, genetic diversity, and evolutionary factors that are presumably shaping the global spread and successful adaptation of PLRV as a destructive potato pathogen to geographically isolated regions of the world.
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Affiliation(s)
- Tahir Farooq
- Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | - Muhammad Dilshad Hussain
- State Key Laboratory for Agro-Biotechnology, and Ministry of Agriculture and Rural Affairs, Key Laboratory for Pest Monitoring and Green Management, Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Muhammad Taimoor Shakeel
- Department of Plant Pathology, Faculty of Agriculture & Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Hasan Riaz
- Institute of Plant Protection, Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan
| | - Ummara Waheed
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan
| | - Maria Siddique
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad, Pakistan
| | - Irum Shahzadi
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad, Pakistan
| | - Muhammad Naveed Aslam
- Department of Plant Pathology, Faculty of Agriculture & Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Yafei Tang
- Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | - Xiaoman She
- Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China,*Correspondence: Xiaoman She, ; Zifu He,
| | - Zifu He
- Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China,*Correspondence: Xiaoman She, ; Zifu He,
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LaTourrette K, Holste NM, Garcia-Ruiz H. Polerovirus genomic variation. Virus Evol 2021; 7:veab102. [PMID: 35299789 PMCID: PMC8923251 DOI: 10.1093/ve/veab102] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 11/21/2021] [Accepted: 12/03/2021] [Indexed: 01/01/2023] Open
Abstract
Abstract
The polerovirus (family Solemoviridae, genus Polerovirus) genome consists of single-, positive-strand RNA organized in overlapping open reading frames (ORFs) that, in addition to others, code for protein 0 (P0, a gene silencing suppressor), a coat protein (CP, ORF3), and a read-through domain (ORF5) that is fused to the CP to form a CP-read-through (RT) protein. The genus Polerovirus contains twenty-six virus species that infect a wide variety of plants from cereals to cucurbits, to peppers. Poleroviruses are transmitted by a wide range of aphid species in the genera Rhopalosiphum, Stiobion, Aphis, and Myzus. Aphid transmission is mediated both by the CP and by the CP-RT. In viruses, mutational robustness and structural flexibility are necessary for maintaining functionality in genetically diverse sets of host plants and vectors. Under this scenario, within a virus genome, mutations preferentially accumulate in areas that are determinants of host adaptation or vector transmission. In this study, we profiled genomic variation in poleroviruses. Consistent with their multifunctional nature, single-nucleotide variation and selection analyses showed that ORFs coding for P0 and the read-through domain within the CP-RT are the most variable and contain the highest frequency of sites under positive selection. An order/disorder analysis showed that protein P0 is not disordered. In contrast, proteins CP-RT and virus protein genome-linked (VPg) contain areas of disorder. Disorder is a property of multifunctional proteins with multiple interaction partners. The results described here suggest that using contrasting mechanisms, P0, VPg, and CP-RT mediate adaptation to host plants and to vectors and are contributors to the broad host and vector range of poleroviruses. Profiling genetic variation across the polerovirus genome has practical applications in diagnostics, breeding for resistance, and identification of susceptibility genes and contributes to our understanding of virus interactions with their host, vectors, and environment.
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Affiliation(s)
- Katherine LaTourrette
- Nebraska Center for Virology, University of Nebraska-Lincoln, 4240 Fair Street, Lincoln, NE 68583, USA
- Department of Plant Pathology, University of Nebraska-Lincoln, 406 Plant Science Hall, Lincoln, NE 68583, USA
- Complex Biosystems Interdisciplinary Life Sciences Program, Institute of Agriculture and Natural Resources, University of Nebraska-Lincoln, 2200 Vine Street, Lincoln, NE 68583, USA
| | - Natalie M Holste
- Nebraska Center for Virology, University of Nebraska-Lincoln, 4240 Fair Street, Lincoln, NE 68583, USA
- Department of Plant Pathology, University of Nebraska-Lincoln, 406 Plant Science Hall, Lincoln, NE 68583, USA
| | - Hernan Garcia-Ruiz
- Nebraska Center for Virology, University of Nebraska-Lincoln, 4240 Fair Street, Lincoln, NE 68583, USA
- Department of Plant Pathology, University of Nebraska-Lincoln, 406 Plant Science Hall, Lincoln, NE 68583, USA
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Sun Q, Shu C, Shi W, Luo Y, Fan G, Nie J, Bi Y, Wang Q, Qi J, Lu J, Zhou Y, Shen Z, Meng Z, Zhang X, Yu Z, Gao S, Wu L, Ma J, Hu S. VarEPS: an evaluation and prewarning system of known and virtual variations of SARS-CoV-2 genomes. Nucleic Acids Res 2021; 50:D888-D897. [PMID: 34634813 PMCID: PMC8728250 DOI: 10.1093/nar/gkab921] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/18/2021] [Accepted: 09/28/2021] [Indexed: 12/17/2022] Open
Abstract
The genomic variations of SARS-CoV-2 continue to emerge and spread worldwide. Some mutant strains show increased transmissibility and virulence, which may cause reduced protection provided by vaccines. Thus, it is necessary to continuously monitor and analyze the genomic variations of SARS-COV-2 genomes. We established an evaluation and prewarning system, SARS-CoV-2 variations evaluation and prewarning system (VarEPS), including known and virtual mutations of SARS-CoV-2 genomes to achieve rapid evaluation of the risks posed by mutant strains. From the perspective of genomics and structural biology, the database comprehensively analyzes the effects of known variations and virtual variations on physicochemical properties, translation efficiency, secondary structure, and binding capacity of ACE2 and neutralizing antibodies. An AI-based algorithm was used to verify the effectiveness of these genomics and structural biology characteristic quantities for risk prediction. This classifier could be further used to group viral strains by their transmissibility and affinity to neutralizing antibodies. This unique resource makes it possible to quickly evaluate the variation risks of key sites, and guide the research and development of vaccines and drugs. The database is freely accessible at www.nmdc.cn/ncovn.
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Affiliation(s)
- Qinglan Sun
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Chang Shu
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenyu Shi
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Yingfeng Luo
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guomei Fan
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Jingyi Nie
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhai Bi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qihui Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yuanchun Zhou
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhihong Shen
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhen Meng
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Xinjiao Zhang
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Zhengfei Yu
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Shenghan Gao
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Linhuan Wu
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Juncai Ma
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Songnian Hu
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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